Insulin promoter factor, and uses related thereto

ABSTRACT

The present invention relates to the discovery in eukaryotic cells, particularly mammalian cells, of novel a transcriptional regulatory factor, referred to hereinafter as &#34;Insulin Promoter Factor 1&#34; or &#34;Ipf1&#34;.

This application is a continuation of Ser. No. 08/320,148, filed Oct. 7,1994, now U.S. Pat. No. 5,849,989, the disclosure of which isincorporated by reference.

BACKGROUND OF THE INVENTION

Each year, over 728,000 new cases of diabetes are diagnosed and 150,000Americans die from the disease and its complications; the total yearlycost in the United States is over 20 billion dollars (Langer et al.(1993) Science 260:920-926). For instance, diabetes is characterized bypancreatic islet destruction or dysfunction leading to loss of glucosecontrol. Diabetes mellitus is a metabolic disorder defined by thepresence of chronically elevated levels of blood glucose(hyperglycemia). Insulin-dependent (Type 1) diabetes mellitus (“IDDM”)results from an autoimmune-mediated destruction of the pancreaticβ-cells with consequent loss of insulin production, which results inhyperglycemia. Type 1 diabetics require insulin replacement therapy toensure survival. Non-insulin-dependent (Type 2) diabetes mellitus(“NIDDM”) is initially characterized by hyperglycemia in the presence ofhigher-than-normal levels of plasma insulin (hyperinsulinemia). In Type2 diabetes, tissue processes which control carbohydrate metabolism arebelieved to have decreased sensitivity to insulin. Progression of theType 2 diabetic state is associated with increasing concentrations ofblood glucose, and coupled with a relative decrease in the rate ofglucose-induced insulin secretion.

The primary aim of treatment in both forms of diabetes mellitus is thesame, namely, the reduction of blood glucose levels to as near normal aspossible. Treatment of Type 1 diabetes involves administration ofreplacement doses of insulin. In contrast, treatment of Type 2 diabetesfrequently does not require administration of insulin. For example,initial therapy of Type 2 diabetes may be based on diet and lifestylechanges augmented by therapy with oral hypoglycemic agents such assulfonylurea. Insulin therapy may be required, however, especially inthe later stages of the disease, to produce control of hyperglycemia inan attempt to minimize complications of the disease.

More recently, tissue-engineering approaches to treatment have focusedon transplanting healthy pancreatic islets, usually encapsulated in amembrane to avoid immune rejection. Three general approaches have beentested in animal models. In the first, a tubular membrane is coiled in ahousing that contained islets. The membrane is connected to a polymergraph that in turn connects the device to blood vessels. By manipulationof the membrane permeability, so as to allow freediffusion of glucoseand insulin back and forth through the membrane, yet block passage ofantibodies and lymphocytes, normoglycemia was maintained inpancreatectomized animals treated with this device (Sullivan et al.(1991) Science 252:718).

In a second approach, hollow fibers containing islet cells wereimmobilized in the polysaccharide alginate. When the device was placeintraperitoneally in diabetic animals, blood glucose levels were loweredand good tissue compatibility was observed (Lacey et al. (1991) Science254:1782).

Finally, islets have been placed in microcapsules composed of alginateor polyacrylates. In some cases, animals treated with thesemicrocapsules maintained normoglycemia for over two years (Lim et al.(1980) Science 210:908; O'Shea et al. (1984) Biochim. Biochys. Acta.840:133; Sugamori et al. (1989) Trans. Am. Soc. Artif. Intern. Organs35:791; Levesque et al. (1992) Endocrinology 130:644; and Lim et al.(1992) Transplantation 53:1180).

However, all of these transplantation strategies require a large,reliable source of donor islets.

SUMMARY OF THE INVENTION

The present invention relates to the discovery in eukaryotic cells,particularly mammalian cells, of novel a transcriptional regulatoryfactor, referred to hereinafter as “Insulin Promoter Factor 1” or“Ipf1”.

In general, the invention features an Ipf1 polypeptide, preferably asubstantially pure preparation of the polypeptide, or a recombinant Ipf1polypeptide. In preferred embodiments the polypeptide has a biologicalactivity associated with its binding to Ipf1-responsive elements, suchas the P1 insulin promoter site, and with its binding to othertranscriptional regulatory proteins. The polypeptide can be identical tothe polypeptide shown in SEQ ID No: 2, or it can merely be homologous tothat sequence. For instance, the polypeptide preferably has an aminoacid sequence at least 60% homologous to the amino acid sequence in SEQID No: 2, though higher sequence homologies of, for example, 80%, 90% or95% are also contemplated. The polypeptide of the present invention cancomprise the full length protein represented in SEQ ID No: 2, or it cancomprise a fragment of that protein, which fragment may be, forinstance, at least 5, 10, 20, 50 or 100 amino acids in length. Thefragment can be derived to include, for example, regions of the proteinwhich are likely to be involved in protein—protein interactions withother transcriptional regulatory proteins or which may influence theDNA-binding specficity of the homeodomain of Ipf1 (Glu146-Ser211)relative to other heterologous homeodomains. For instance, the fragmentcan include at least 4 amino acid residues between Metl to Glu145 and/orSer212 to Arg284, though more preferably includes portions of at least10, 20, 30 or 50 residues from one or both of those regions. Exemplaryfragments include N-terminal fragments within or including Met1 toGlu145, or C-terminal fragments within or including Glu146 to Arg284.

Moreover, as described below, the Ipf1 polypeptide of the presentinvention can be either an agonist (e.g. mimics), or alternatively, anantagonist of a biological activity of a naturally occurring form ofIpf1. That is, the polypeptide is an Ipf1 homolog which is able tomodulate Ipf1-mediated gene expression (e.g., a gene containing anIpf1-responsive element) in at least one tissue in which wild-type Ipf1is expressed, such as in pancreatic tissue, particularly β-islet cells.

In a preferred embodiment, a peptide having at least one biologicalactivity of the subject polypeptide may differ in amino acid sequencefrom the sequence in SEQ ID No: 2, but such differences result in amodified protein which functions in the same or similar manner as thenative Ipf1 or which has the same or similar characteristics of thenative Ipf1. Moreover, homologs of the naturally occurring protein arecontemplated which are antagonistic of the normal cellular role of thenaturally occurring form of Ipf1. For example, the homolog may becapable of interfering with the ability of wild-type Ipf1 to modulategene expression, e.g. of developmentally or growth regulated genes.Preferred antagonistic forms of an Ipf1 polypeptide either (i) retainsthe DNA binding ability of authentic Ipf1 but lack the ability toassemble transcriptionally-competent protein complexes, or (ii) lacksDNA binding ability (e.g. to Ipf1-RE2) yet retains the ability to bindto other transcription regulatory complexes normally involving authenticIpf1.

In yet other preferred embodiments, the Ipf1 polypeptide is arecombinant fusion protein which includes a second polypeptide portion,e.g., a second polypeptide having an amino acid sequence unrelated toIpf1, e.g. the second polypeptide portion is glutathione-S-transferase,e.g. the second polypeptide portion is a DNA binding domain of aheterologous transcriptional regulatory protein, or the secondpolypeptide portion is an RNA polymerase activating domain, e.g. thefusion protein is functional in a two-hybrid assay.

Yet another aspect of the present invention concerns an immunogencomprising an Ipf1 peptide in an immunogenic preparation, the immunogenbeing capable of eliciting an immune response specific for said Ipf1polypeptide. The response can be in the form of a humoral response, e.g.an antibody response or a cellular response. In preferred embodiments,the immunogen comprising an antigenic determinant, e.g. a uniquedeterminant, from a protein represented by SEQ ID No: 2.

A still further aspect of the present invention features an antibodypreparation specifically reactive with an epitope of an Ipf1polypeptide, such as an Ipf1 immunogen.

Another aspect of the present invention provides a substantiallyisolated nucleic acid having a nucleotide sequence which encodes an Ipf1polypeptide. In preferred embodiments: the encoded polypeptidespecifically binds an Ipf1-responsive element, and/or is able to eitheragonize or antagonize assembly of Ipf1-dependent transcriptional proteincomplexes. The coding sequence of the nucleic acid can comprise anIpf1-encoding sequence which can be identical to the cDNA shown in SEQID No: 1, or it can merely be homologous to that sequence. For instance,the Ipf1-encoding sequence preferably has a sequence at least 60%homologous to the nucleotide sequence in SEQ ID No: 1, though highersequence homologies of, for example, 80%, 90% or 95% are alsocontemplated. The polypeptide encoded by the nucleic acid can comprisethe nucleotide sequence represented in SEQ ID No: 1 which encodes thefull length protein, or it can comprise a fragment of that nucleic acid,which fragment may be, for instance, a fragment of the full length Ipf1protein which is, for example, at least 5, 10, 20, 50 or 100 amino acidsin length. The polypeptide encoded by the nucleic acid can be either anagonist (e.g. mimics), or alternatively, an antagonist of a biologicalactivity of a naturally occurring form of the Ipf1 protein, e.g., thepolypeptide is able to modulate Ipf1-dependent gene expression in atleast one tissue in which the Ipf1 protein is expressed, such as inpancreatic tissue.

Furthermore, in certain preferred embodiments, the subject Ipf1 nucleicacid will include a transcriptional regulatory sequence, e.g. at leastone of a transcriptional promoter or transcriptional enhancer sequence,which regulatory sequence is operably linked to the Ipf1 gene sequence.Such regulatory sequences can be used in to render the Ipf1 genesequence suitable for use as an expression vector.

In yet a further preferred embodiment, the nucleic acid hybridizes understringent conditions to a nucleic acid probe corresponding to at least12 consecutive nucleotides of SEQ ID No: 1; preferably to at least 20consecutive nucleotides of SEQ ID No: 1; more preferably to at least 40consecutive nucleotides of SEQ ID No: 1.

The invention also features transgenic non-human animals, e.g. mice,rats, rabbits or pigs, having a transgene, e.g., animals which include(and preferably express) a heterologous form of the Ipf1 genes describedherein, e.g. a gene derived from humans, or which misexpress anendogenous Ipf1 gene, e.g., an animal in which expression of the subjectIpf1 protein is disrupted. Such a transgenic animal can serve as ananimal model for studying cellular disorders comprising mutated ormis-expressed Ipf1 alleles or for use in drug screening.

The invention also provides a probe/primer comprising a substantiallypurified oligonucleotide, wherein the oligonucleotide comprises a regionof nucleotide sequence which hybridizes under stringent conditions to atleast 10 consecutive nucleotides of sense or antisense sequence of oneof SEQ ID No: 1, or naturally occurring mutants thereof. In preferredembodiments, the probe/primer further includes a label group attachedthereto and able to be detected. The label group can be selected, e.g.,from a group consisting of radioisotopes, fluorescent compounds,enzymes, and enzyme co-factors. Probes of the invention can be used as apart of a diagnostic test kit for identifying β-islet cells includingabnormal β-cells, as well as abnormal pancreatic tissues. For instance,the probe can be employed for detecting, in a sample of cells isolatedfrom a patient, a level of a nucleic acid encoding the subject Ipf1protein or mutated forms thereof; e.g. measuring the Ipf1 mRNA level ina cell, or determining whether the genomic Ipf1 gene has been mutated ordeleted. Preferably, the oligonucleotide is at least 10 nucleotides inlength, though primers of 20, 30, 50, 100, or 150 nucleotides in lengthare also contemplated.

In yet another aspect, the invention provides an assay for screeningtest compounds for an inhibitor, or alternatively, a potentiator, of aninteraction between an Ipf1 and an Ipf1-responsive element (such as a P1promoter), or with other transcriptional regulatory proteins. Anexemplary method includes the steps of (i) combining an Ipf1 protein, atest compound, and an Ipf1-target molecule, under conditions wherein,but for the test compound, the Ipf1 protein and the Ipf1-target moleculeare able to interact; and (ii) detecting the formation of a complexwhich includes the Ipf1 protein and the target molecule. A statisticallysignificant change, such as a decrease, in the formation of the complexin the presence of a test compound (relative to what is seen in theabsence of the test compound) is indicative of a modulation, e.g.,inhibition, of the interaction between Ipf1 and the target molecule. Inpreferred embodiments, the target molecule is an Ipf1-responsiveelement, e.g., a nucleic acid comprising an Ipf1 binding sequence, suchas an insulin P1 promoter sequence. In alternative embodiments, thetarget molecule is a protein which binds Ipf1, such as a proteininvolved in forming transcriptional regulatory complexes with Ipf1.Moreover, primary screens are provided in which the target molecule andIpf1 are combined in a cell-free system and contacted with the testcompound; i.e. the cell-free system is selected from a group consistingof a cell lysate and a reconstituted protein:DNA or protein:proteinmixture. Alternatively, the target molecule and Ipf1 protein aresimultaneously provided in a cell, and the cell is contacted with thetest compound. For example, where the target molecule is a nucleic acidcomprising an Ipf1-responsive element, the expression of a marker genecontrolled by the Ipf1-responsive element is detected.

The present invention also provides a method for treating an animal,including a human, having a disorder characterized by a loss of, orabnormal control of, wild-type function of Ipf1, comprisingadministering an effective amount of an Ipf1 agonist. In one embodiment,the method comprises administering a nucleic acid construct encoding apolypeptide represented in SEQ ID No: 2, under conditions whcrein theconstruct is incorporated by cells deficient in insulin production, andunder conditions wherein the recombinant gene is expressed, e.g. by genetherapy techniques. In other embodiments, the action of anaturally-occurring Ipf1 protein is antagonized by therapeuticexpression of an Ipf1 homolog which is an antagonistic of, for example,assembly of functional Ipf1 transcriptional regulatory complexes, or bydelivery of an antisense nucleic acid molecule which inhibits IPFtranscriptional regulation. Such techniques can likewise be used totreat a disorder characterized by abherent or unwanted expression of agene regulated by an Ipf1-RE, such as an insulin gene.

Another aspect of the present invention provides a method of determiningif a subject, e.g. a human patient, is at risk for a disordercharacterized by unwanted cell proliferation or differentiation. Themethod includes detecting, in a tissue of the subject, the presence orabsence of a genetic lesion characterized by at least one of (i) amutation of a gene encoding a protein represented by SEQ ID No: 2, or ahomolog thereof; (ii) the mis-expression of a gene encoding a proteinrepresented by SEQ ID No: 2; or (iii) the mis-incorporation of Ipf1 in atranscriptional regulatory complex. In preferred embodiments: detectingthe genetic lesion includes ascertaining the existence of at least oneof: a deletion of one or more nucleotides from the Ipf1 gene; anaddition of one or more nucleotides to the gene, an substitution of oneor more nucleotides of the gene, a gross chromosomal rearrangement ofthe gene; an alteration in the level of a messenger RNA transcript ofthe gene; the presence of a non-wild type splicing pattern of amessenger RNA transcript of the gene; or a non-wild type level of theprotein.

For example, detecting the genetic lesion can include (i) providing aprobe/primer including an oligonucleotide containing a region ofnucleotide sequence which hybridizes to a sense or antisense sequence ofSEQ ID No: 1, or naturally occurring mutants thereof or 5′ or 3′flanking sequences naturally associated with the Ipf1 gene; (ii)exposing the probe/primer to nucleic acid of the tissue; and (iii)detecting, by hybridization of the probe/primer to the nucleic acid, thepresence or absence of the genetic lesion; e.g. wherein detecting thelesion comprises utilizing the probe/primer to determine the nucleotidesequence of the Ipf1 gene and, optionally, of the flanking nucleic acidsequences. For instance, the probe/primer can be employed in apolymerase chain reaction (PCR) or in a ligation chain reaction (LCR).In alternate embodiments, the level of Ipf1 protein and/or itsparticipation in complexes is detected in an immunoassay using anantibody which is specifically immunoreactive with a protein representedby SEQ ID No: 2.

The invention also features transgenic non-human animals, e.g. mice,rats, rabbits or pigs, harboring in one or more of its cells anIpf1-encoding transgene. In preferred embodiments, the transgene isexpressed, causing Ipf1-dependent gene transcription where the transgeneencodes an agonistic form of the protein, or disruption of Ipf1-inducedexpression where the transgene encodes an antagonistic form of theprotein. Such transgenic animals can serve as models for studyingcellular and tissue disorders comprising mutated or mis-expressed Ipf1alleles, as well as for studying the physiological role of Ipf1 inproliferation, differentiation and maintenance of tissues in vivo inboth adult and embryonic systems. Furthermore, inhibition of Ipf1expression in certain cells, such as β-cells, can be used to unravel theeffects of various autocrine and paracrine functions of pancreatichormones, and can be used in drug screening assays designed to detectmodulators of these other factors.

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of cell biology, cell culture,molecular biology, transgenic biology, microbiology, recombinant DNA,and immunology, which are within the skill of the art. Such techniquesare explained fully in the literature. See, for example, MolecularCloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch andManiatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning,Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M.J. Gait ed., 1984); Mullis et al. U.S. Pat. No.: 4,683,195; Nucleic AcidHybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription AndTranslation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of AnimalCells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells AndEnzymes (IRL Press, 1986); B. Perbal, A Practical Guide To MolecularCloning (1984); the treatise, Methods In Enzymology (Academic Press,Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller andM. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods InEnzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical MethodsIn Cell And Molecular Biology (Mayer and Walker, eds., Academic Press,London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo,(Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).Other references include Ohlsson et al. (1993) EMBO J 12:4251-4259;Ohlsson et al. (1991) Mol Endo 5:897-904; Walker et al. (1983) Nature306:557-561; Leonard et al. (1993) Mol Endo 7:1275-1283: Miller et al.(1994) EMBO J 13:1145-1156; and Harrison et al. (1994) J Biol Chem269:19968-19975, all of which are incorporated by reference herein.

Other features and advantages of the invention will be apparent from thefollowing detailed description, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIGS. 1A, 1B and 1C illustrate the results of expression of the Ipf1gene in both β-cells and non-β-cells transactivates a reporter constructvia the P1 site. (FIG. 1A) Mutation of the P1 promoter site results in adecreased activity for the rat insulin I 5′ flank and the stimulation ofthe activity of the 5′ flank as a result of Ipf1 expression iscritically dependent on an intact P1 site. RSV and RSV/Ipf1 recombinantexpression vectors were co-transfected with the Tk-CAT, Ins-CAT andP1mut #2/Ins-CAT reporter genes into βTC1 cells using an internalcontrol β-gal plasmid as described previously (Walker et al. (1983)Nature 306:557-581). (FIG. 1B) Multimers of the P1 site in front of areporter gene is specifically trans-activated by the expression of theIpf1 gene in heterologous cells. RSV, RSV-Ipf1 and RSV-Isl1 recombinantexpression vectors were co-transfected with the β-globin-CAT and 5×P1β-globin-CAT construct in CHO cells. (FIG. 1C) Overexpression of theIpf1 gene in βTC1 cells results in a further up-regulation of theactivity of the P1 element. RSV and RSV-Ipf1 recombinant expressionvectors were co-transfected with the β-globin-CAT and 5×P1 β-globin-CATconstruct in βTC1 cells. The numbers given are normalized to theinternal control and represent the mean of at least five independenttransfection experiments. In all cases, the standard error of the meanwas <15% of this value.

FIG. 2 is a schematic representation of targeting construct, genomic DNAand the expected product of homologous recombination. The two exons ofIpf1 are indicated by cylinders and the bacterial neomycin gene, undercontrol of the herpes simplex virus (HSV) promoter/enhancer, isrepresented by a triangular bar. Deletion of the 3.1-kb HindIII/Ncolfragment from within the 7.2-kb BamH1 segment of the Ipf1 genomic DNAresults in loss of the entire homeobox, the splice acceptor site andparts of the intron. This fragment was replaced with the 1,142-bpXnol/BamH1 fragment from pMC1 neopoly(A) (Thomas et al. (1987) Cell51:503-512). Restriction enzymes: B, BamH1; H, HindIII; N. Ncol; P.Pstl. The mouse Ipf1 gene was cloned from a mouse 129/SV genomiclibrary. E14-1 ES cells were cultured on mitomycin-treated embryonicfibroblasts in medium supplemented with 1,000 U/ml leukaemia-inhibitoryfactor as previously described (Kuhn et al. (1991) Science 254:707-710).A Bio-Rad GenePulser at 500 F, 260 mV was used to electroporate 10⁷cells with 25 μg ml linearized targeting DNA. Cells were plated onmitomycin-treated neomycin-resistant STO fibroblasts. Selection with 250μg ml G418 was initiated after 48 h and ES colonies were picked eightdays later. Blastocysts from C57BL/6 mice were injected and transferredto pseudopregnant (C57BL/6×CBA)F₁ females to generate chimaericoffspring as described in Hogan et al. in Manipulating the Mouse Embryo,(Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

DETAILED DESCRIPTION OF THE INVENTION

The endocrine pancreas of mammals is composed of several thousand isletsof Langherhans. Each individual islet contains four hormone-producingcell types in a characteristic proportion and distribution, with thedifferent hormone-producing cells appearing sequentially during embryogenesis (Pictet et al. (1972) in Steiner, D. F. and Frenkel, M.(EDS),Handbook of Physiology, Series 7, American Physiology Society,Washington, D.C., pp. 25-66; Yoshinari et al. (1992) Anat. Embryol.165:63-70; Titelman et al. (1987) Dev. Biol. 121:454-466; Herrera et al.(1991) Development 113:1257-1265; Gitts et al. (1992) PNAS89:1128-1132). Although the precise lineage relationship between thedifferent islet cells is not known, co-expression of different hormonegenes during normal pancreas development and in cloned cell-linesderived from islet cell tumors suggests a common precursor for thepancreatic endocrine cells (Medsen et al. (1986) J. Cell Biol.103:2025-2034; Alpert et al. (1988) Cell 53:295-308; and Herrera et al.Supra). These observations have suggested that terminal differentiation,restricting the expression of the hormone genes to the individualendocrine cell-type, occurs relatively late in the ontogeny of theendocrine pancreas.

For some of these hormone genes it has been possible to identify thecis- and trans-acting elements that regulate the islet-specificexpression of the genes. For instance, the insulin-1 gene containsapproximately 350 basepairs of 5′ flanking DNA (e.g., the “insulintranscriptional regulatory sequence”) which is sufficient for selective,β-cell specific expression both in cell lines and in transgenic animals(Walker et al. (1983) Nature 306:557-581; and Alpert et al., supra),with both a strong β-cell enhancer and a promoter element containedwithin these 350 basepairs (Edlund et al. (1983) Science 230:912-916;and Karlson et al. (1987) PNAS 84:8819-8823).

This invention, as described below, derives in part from the cloning ofa mamalian transcriptional regulatory protein which binds to andactivates transcription from the insulin transcriptional regulatorysequence. This transcriptional regulatory factor, referred tohereinafter as “Insulin Promoter Factor 1” or “Ipf1” is apparently partof the mechanism involved in developmental coordination of endodermdifferentiation, particularly of the pancreas and other tissues derivedfrom the primative gut. For instance, as described in the appendedexamples, analysis of Ipf1 expression patterns demonstrate that Ipf1expression occurs in the developing foregut endoderm when this tissuecommits to a pancreatic fate. Moreover, transgenic animals in which Ipf1expression is disrupted selectively lack a pancreas. These findings showthat Ipf1 is needed for the formation of the pancreas, and stronglyimplicates Ipf1 function in the determination and/or maintenance of thepancreatic identity of common precursor cells, and/or in the regulationof their propagation. Ipf1-mediated gene expression is presumablyimportant in the pathogenesis of diabetes and other abnormal glycemicdisease states, and may also be of significance in the progression andpathology of other proliferative or differentiative disorders.Consequently, the interaction of Ipf1 with Ipf1-responsive elements, aswell as with other regulatory proteins, may be significant in themodulation of cellular homeostasis, in the control of organogenesis,and/or in the maintenance of differentiated tissues, as well as in thedevelopment of tissue failure and neoplastic disorders.

Accordingly, certain aspects of the present invention relate todiagnostic and therapeutic assays and reagents for detecting andtreating disorders involving abherent assembly of Ipf1 transcriptionalcomplexes. Moreover, drug discovery assays are provided for identifyingagents which can modulate the binding of Ipf1 with other transcriptionalregulatory proteins or with Ipf1 responsive elements. Such agents can beuseful therapeutically to alter the growth and/or differentiation ofpancreatic cell. Other aspects of the invention are described below orwill be apparent to those skilled in the art in light of the presentdisclosure.

For convenience, certain terms employed in the specification, examples,and appended claims are collected here.

As used herein, the term “nucleic acid” refers to polynucleotides suchas deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid(RNA). The term should also be understood to include, as equivalents,analogs of either RNA or DNA made from nucleotide analogs, and, asapplicable to the embodiment being described, single-stranded (such assense or antisense) and double-stranded polynucleotides.

As used herein, the term “gene” or “recombinant gene” refers to anucleic acid comprising an open reading frame encoding an insulinpromoter factor of the present invention, including both exon and(optionally) intron sequences. A “recombinant gene” refers to nucleicacid encoding Ipf1 and comprising Ipf1-encoding exon sequences, thoughit may optionally include intron sequences which are either derived froma chromosomal Ipf1 gene or from an unrelated chromosomal gene. Anexemplary Ipf1 recombinant gene is represented by any one of SEQ IDNo: 1. The term “intron” refers to a DNA sequence present in a givenIpf1 gene which is not translated into protein and is generally foundbetween exons.

As used herein, the term “transfection” means the introduction of anucleic acid, e.g., an expression vector, into a recipient cell bynucleic acid-mediated gene transfer. “Transformation”, as used herein,refers to a process in which a cell's genotype is changed as a result ofthe cellular uptake of exogenous DNA or RNA, and, for example, thetransformed cell expresses a recombinant form of Ipf1, or whereanti-sense expression occurs, from the transferred gene, the expressionof a naturally-occurring form of Ipf1 is disrupted.

As used herein, the term “vector” refers to a nucleic acid moleculecapable of transporting another nucleic acid to which it has beenlinked. One type of preferred vector is an episome, i.e., a nucleic acidcapable of extra-chromosomal replication. Preferred vectors are thosecapable of autonomous replication and/expression of nucleic acids towhich they are linked. Vectors capable of directing the expression ofgenes to which they are operatively linked are referred to herein as“expression vectors”. In general, expression vectors of utility inrecombinant DNA techniques are often in the form of “plasmids” whichrefer to circular double stranded DNA loops which, in their vector formare not bound to the chromosome. In the present specification, “plasmid”and “vector” are used interchangeably as the plasmid is the mostcommonly used form of vector. However, the invention is intended toinclude such other forms of expression vectors which serve equivalentfunctions and which become known in the art subsequently hereto.

“Transcriptional regulatory sequence” is a generic term used throughoutthe specification to refer to DNA sequences, such as initiation signals,enhancers, and promoters, which induce or control transcription ofprotein coding sequences with which they are operably linked. Inpreferred embodiments, transcription of a recombinant Ipf1 gene is underthe control of a promoter sequence (or other transcriptional regulatorysequence) which controls the expression of the recombinant gene in acell-type in which expression is intended. It will also be understoodthat the recombinant gene can be under the control of transcriptionalregulatory sequences which are the same or which are different fromthose sequences which control transcription of a naturally-occurringform of Ipf1.

As used herein, the term “Ipf1-responsive element” or “Ipf1-RE” refersto a transcriptional regulatory sequence which controls expression of agene in an Ipf1-dependent manner. That is, the Ipf1-RE has a nucleotidesequence which is specifically bound by an Ipf1 protein, and the bindingof Ipf1 regulates expression of a gene operably linked to the Ipf1-RE.An exemplary Ipf1-RE is the 5′ flanking transcriptional regulation DNAof the insulin I gene, particularly the P1 promoter site5′-GCCCTTAATGGGCCAA, or its core sequence TAATGGG.

As used herein, the term “tissue-specific promoter” means a DNA sequencethat serves as a promoter, i.e., regulates expression of a selected DNAsequence operably linked to the promoter, and which effects expressionof the selected DNA sequence in specific cells of a tissue, such ascells of a urogenital origin, e.g. renal cells, or cells of a neuralorigin, e.g. neuronal cells. The term also covers so-called “leaky”promoters, which regulate expression of a selected DNA primarily in onetissue, but cause expression in other tissues as well.

As used herein, a “transgenic animal” is any animal, preferably anon-human mammal, bird or an amphibian, in which one or more of thecells of the animal contain heterologous nucleic acid introduced by wayof human intervention, such as by trangenic techniques well known in theart. The nucleic acid is introduced into the cell, directly orindirectly by introduction into a precursor of the cell, by way ofdeliberate genetic manipulation, such as by microinjection or byinfection with a recombinant virus. The term genetic manipulation doesnot include classical cross-breeding, or in vitro fertilization, butrather is directed to the introduction of a recombinant DNA molecule.This molecule may be integrated within a chromosome, or it may beextrachromosomally replicating DNA. In the typical transgenic animalsdescribed herein, the transgene causes cells to express, a recombinantform of Ipf1, e.g. either agonistic or antagonistic forms. However,transgenic animals in which the recombinant Ipf1 gene is silent are alsocontemplated, as for example, the FLP or CRE recombinase dependentconstructs described below. Transgenic animals also include bothconstitutive and conditional “knock out” animals. The “non-humananimals” of the invention include vertebrates such as rodents, non-humanprimates, sheep, dog, cow, chickens, amphibians, reptiles, etc.Preferred non-human animals are selected from the rodent familyincluding rat and mouse, most preferably mouse. The term “chimericanimal” is used herein to refer to animals in which the recombinant geneis found, or in which the recombinant is expressed in some but not allcells of the animal. The term “tissue-specific chimeric animal”indicates that the recombinant Ipf1 gene is present and/or expressed insome tissues but not others.

As used herein, the term “transgene” means a nucleic acid sequence(encoding, e.g., a Ipf1), which is partly or entirely heterologous,i.e., foreign, to the transgenic animal or cell into which it isintroduced, or, is homologous to an endogenous gene of the transgenicanimal or cell into which it is introduced, but which is designed to beinserted, or is inserted, into the animal's genome in such a way as toalter the genome of the cell into which it is inserted (e.g., it isinserted at a location which differs from that of the natural gene orits insertion results in a knockout or other loss-of-function mutation).A transgene can include one or more transcriptional regulatory sequencesand any other nucleic acid, such as introns, that may be necessary foroptimal expression of a selected nucleic acid.

As is well known, genes for a particular polypeptide may exist in singleor multiple copies within the genome of an individual. Such duplicategenes may be identical or may have certain modifications, includingnucleotide substitutions, additions or deletions, which all still codefor polypeptides having substantially the same activity. The term “DNAsequence encoding an Ipf1 polypeptide” may thus refer to one or moregenes within a particular individual. Moreover, certain differences innucleotide sequences may exist between individual organisms, which arecalled alleles. Such allelic differences may or may not result indifferences in amino acid sequence of the encoded polypeptide yet stillencode a protein with the same biological activity.

“Homology” refers to sequence similarity between two peptides or betweentwo nucleic acid molecules. Homology can be determined by comparing aposition in each sequence which may be aligned for purposes ofcomparison. When a position in the compared sequence is occupied by thesame base or amino acid, then the molecules are homologous at thatposition. A degree of homology between sequences is a function of thenumber of matching or homologous positions shared by the sequences.

“Cells,” “host cells” or “recombinant host cells” are terms usedinterchangeably herein. It is understood that such terms refer not onlyto the particular subject cell but to the progeny or potential progenyof such a cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

A “chimeric protein” or “fusion protein” is a fusion of a first aminoacid sequence encoding an Ipf1 polypeptide with a second amino acidsequence defining a domain foreign to and not substantially homologouswith any domain of the subject Ipf1. A chimeric protein may present aforeign domain which is found (albeit in a different protein) in anorganism which also expresses the first protein, or it may be an“interspecies”, “intergenic”, etc. fusion of protein structuresexpressed by different kinds of organisms.

The term “evolutionarily related to”, with respect to nucleic acidsequences encoding Ipf1, refers to nucleic acid sequences which havearisen naturally in an organism, including naturally occurring mutants.The term also refers to nucleic acid sequences which, while derived froma naturally occurring Ipf1, have been altered by mutagenesis, as forexample, combinatorial mutagenesis described below, yet still encodepolypeptides which have at least one activity of a Ipf1.

The term “isolated” as also used herein with respect to nucleic acids,such as DNA or RNA, refers to molecules separated from other DNAs, orRNAs, respectively, that are present in the natural source of themacromolecule. For example, an isolated nucleic acid encoding one of thesubject Ipf1 preferably includes no more than 10 kilobases (kb) ofnucleic acid sequence which naturally immediately flanks that particularIpf1 gene in genomic DNA, more preferably no more than 5 kb of suchnaturally occurring flanking sequences, and most preferably less than1.5 kb of such naturally occurring flanking sequence. The term isolatedas used herein also refers to a nucleic acid or peptide that issubstantially free of cellular material, viral material, or culturemedium when produced by recombinant DNA techniques, or chemicalprecursors or other chemicals when chemically synthesized. Moreover, an“isolated nucleic acid” is meant to include nucleic acid fragments whichare not naturally occurring as fragments and would not be found in thenatural state.

As described below, one aspect of the invention pertains to an isolatednucleic acid comprising the nucleotide sequence encoding an Ipf1polypeptide, and/or equivalents of such nucleic acids. The term nucleicacid as used herein is intended to include fragments and equivalents.The term equivalent is understood to include nucleotide sequencesencoding functionally equivalent Ipf1 molecules or functionallyequivalent polypeptides which, for example, retain the ability to bindto other transcriptional regulatory proteins or to transcriptionalregulatory sequences of, for example, an insulin gene. Equivalentnucleotide sequences will include sequences that differ by one or morenucleotide substitutions, additions or deletions, such as allelicvariants; and will, therefore, include sequences that differ from thenucleotide sequence of Ipf1 shown in SEQ ID No: 1 due to the degeneracyof the genetic code. Equivalents will also include nucleotide sequenceswhich hybridize under stringent conditions (i.e., equivalent to about20-27° C. below the melting temperature (T_(m)) of the DNA duplex formedin about 1M salt) to the nucleotide sequence represented in SEQ IDNo: 1. In one embodiment, equivalents will further include nucleic acidsequences derived from or otherwise related to, the nucleotide sequenceshown SEQ ID No: 1.

For example, it will be generally appreciated that, under certaincircumstances, it may be advantageous to provide homologs of the subjectIpf1 protein which, while not identical to SEQ ID No.: 2, function as anIpf1 agonist or an Ipf1 antagonist, in order to promote or inhibit thebiological activities of the naturally-occurring form of the protein.For instance, antagonistic homologs can be generated which interferewith the ability of wild-type (“authentic”) Ipf1 to form transcriptionalactivating complexes at Ipf1-responsive elements. As described below, anantagonistic Ipf1 homolog, such as a truncation mutant which retainsDNA-binding activity yet is transcriptionally defective, can be used inthe treatment of, for example, hyperinsulinemia.

A polypeptide is considered to possess a biological activity of Ipf1 ifthe polypeptide has one or more of the following properties: the abilityto modulate at least one of proliferation, differentiation or suvival ofa cell which expresses a gene that is transcriptionally regulated by anIpf1-RE; the ability to modulate gene expression of a gene that istranscriptionally regulated by an Ipf1-RE, e.g. of a developmentally orgrowth regulated gene, e.g. of an insulin gene; the ability to modulategene expression in pancreatic tissue, e.g. in the ability to bind to theability agonize or antagonize assembly of Ipf1-containingtranscriptional protein complexes. An Ipf1 polypeptide may additionallybe characterized by the ability to modulate differentiation ofendodermally-derived tissue, such as tissue derived from the primitivegut, e.g. pancreatic tissue, e.g. β-cells. A protein also has Ipf1biological activity if it is a specific agonist or antagonist of one ofthe above recited properties.

Preferred nucleic acids encode an Ipf1 polypeptide comprising an aminoacid sequence at least 60% homologous, more preferably 70% homologousand most preferably 80% homologous with an amino acid sequence shown inone of SEQ ID No: 2. Nucleic acids which encode polypeptides that retainan activity of Ipf1 and having at least about 90%, more preferably atleast about 95%, and most preferably at least about 98-99% homology witha sequence shown in one of SEQ ID No: 2 are also within the scope of theinvention, as of course are proteins which are identical to theaforementioned sequence listings. In one embodiment, the nucleic acid isa cDNA encoding a peptide having at least one activity of the subjectIpf1 protein. Preferably, the nucleic acid is a cDNA molecule comprisingat least a portion of the nucleotide sequence represented in one of SEQID No: 1. A preferred portion of these cDNA molecules includes thecoding region of the gene.

Another aspect of the invention provides a nucleic acid which hybridizesunder high or low stringency conditions to a DNA or RNA which encodes apeptide having all or a portion of the amino acid sequence shown in SEQID No: 2. Appropriate stringency conditions which promote DNAhybridization, for example, 6.0×sodium chloride/sodium citrate (SSC) atabout 45° C., followed by a wash of 2.0×SSC at 50° C., are known tothose skilled in the art or can be found in Current Protocols inMolecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Forexample, the salt concentration in the wash step can be selected from alow stringency of about 2.0×SSC at 50° C. to a high stringency of about0.2×SSC at 50° C. In addition, the temperature in the wash step can beincreased from low stringency conditions at room temperature, about 22°C., to high stringency conditions at about 65° C.

Nucleic acids which have a sequence that differ from the nucleotidesequence shown in SEQ ID No: 1 due to degeneracy in the genetic code arealso within the scope of the invention. Such nucleic acids encodefunctionally equivalent peptides (i.e., a peptide having a biologicalactivity of a Ipf1) but that differ in sequence from said sequencelistings due to degeneracy in the genetic code. For example, a number ofamino acids are designated by more than one triplet. Codons that specifythe same amino acid, or synonyms (for example, CAU and CAC each encodehistidine) may result in “silent” mutations which do not affect theamino acid sequence of Ipf1 polypeptide. However, it is expected thatDNA sequence polymorphisms that do lead to changes in the amino acidsequences of the subject Ipf1 will exist among vertebrates. One skilledin the art will appreciate that these variations in one or morenucleotides (up to about 3-5% of the nucleotides) of the nucleic acidsencoding lpf1 polypeptides Ipf1 may exist among individuals of a givenspecies due to natural allelic variation. Any and all such nucleotidevariations and resulting amino acid polymorphisms are within the scopeof this invention.

Fragments of the nucleic acid encoding the subject Ipf1 are also withinthe scope of the invention. As used herein, a fragment encoding theactive portion of a Ipf1 refers to a nucleic acid having fewernucleotides than the nucleotide sequence encoding the entire amino acidsequence of Ipf1 but which nevertheless encodes a peptide which iseither an agonist or antagonist of authentic Ipf1, e.g. the fragmentretains the ability to bind to an insulin promoter. Nucleic acidfragments within the scope of the present invention include thosecapable of hybridizing under high or low stringency conditions withnucleic acids from other species for use in screening protocols todetect Ipf1 homologs, including alternate isoforms, e.g. mRNA splicingvariants. Nucleic acids within the scope of the invention may alsocontain linker sequences, modified restriction endonuclease sites andother sequences useful for molecular cloning, expression or purificationof recombinant forms of the subject Ipf1 protein.

As indicated by the examples set out below, a nucleic acid encoding Ipf1or a homologous gene thereof may be obtained from mRNA present in any ofa number of eukaryotic cells. It should also be possible to obtainnucleic acids encoding Ipf1 from genomic DNA obtained from both adultsand embryos. For example, a gene encoding Ipf1 can be cloned from eithera cDNA or a genomic library in accordance with protocols hereindescribed, as well as those generally known to persons skilled in theart. A cDNA encoding a Ipf1 can be obtained by isolating total mRNA froma cell, e.g. a mammalian cell, e.g. a human cell. Double stranded cDNAscan then be prepared from the total mRNA, and subsequently inserted intoa suitable plasmid or bacteriophage vector using any one of a number ofknown techniques. The gene encoding the Ipf1 can also be cloned usingestablished polymerase chain reaction techniques in accordance with thenucleotide sequence information provided by the invention. The nucleicacid of the invention can be DNA or RNA. A preferred nucleic acid is acDNA represented by the sequence shown in SEQ ID No: 1.

Another aspect of the invention relates to the use of the isolatednucleic acid in “antisense” therapy. As used herein, “antisense” therapyrefers to administration or in situ generation of oligonucleotide probesor their derivatives which specifically hybridizes (e.g. binds) undercellular conditions, with the cellular mRNA and/or genomic DNA encodingan Ipf1 protein so as to inhibit expression of that protein, e.g. byinhibiting transcription and/or translation. The binding may be byconventional base pair complementarity, or, for example, in the case ofbinding to DNA duplexes, through specific interactions in the majorgroove of the double helix. In general, “antisense” therapy refers tothe range of techniques generally employed in the art, and includes anytherapy which relies on specific binding to oligonucleotide sequences.

An antisense construct of the present invention can be delivered, forexample, as an expression plasmid which, when transcribed in the cell,produces RNA which is complementary to at least a unique portion of thecellular mRNA which encodes an Ipf1 protein. Alternatively, theantisense construct can be an oligonucleotide probe which is generatedex vivo and which, when introduced into the cell causes inhibition ofexpression by hybridizing with the mRNA and/or genomic sequences of anIpf1 gene. Such oligonucleotide probes are preferably modifiedoligonucleotides which are resistant to endogenous nucleases, e.g.exonucleases and/or endonucleases, and is therefore stable in vivo.Exemplary nucleic acid molecules for use as antisense oligonucleotidesare phosphoramidate, phosphothioate and methylphosphonate analogs of DNA(see also U.S. Pat. Nos. 5,176,996; 5,264,564; and 5,256,775).Additionally, general approaches to constructing oligomers useful inantisense therapy have been reviewed, for example, by van der Krol etal. (1988) Biotechniques 6:958-976; and Stein et al. (1988) Cancer Res48:2659-2668.

Accordingly, the modified oligomers of the invention are useful intherapeutic, diagnostic, and research contexts. In therapeuticapplications, the oligomers are utilized in a manner appropriate forantisense therapy in general. For such therapy, the oligomers of theinvention can be formulated for a variety of loads of administration,including systemic and topical or localized administration. Techniquesand formulations generally may be found in Remmington's PharmaceuticalSciences, Meade Publishing Co., Easton, Pa., and may include both humanand vetinary formulations. For systemic administration, injection ispreferred, including intramuscular, intravenous, intraperitoneal, andsubcutaneous for injection, the oligomers of the invention can beformulated in liquid solutions, preferably in physiologically compatiblebuffers such as Hank's solution or Ringer's solution. In addition, theoligomers may be formulated in solid form and redissolved or suspendedimmediately prior to use. Lyophilized forms are also included.

In addition to use in therapy, the oligomers of the invention may beused as diagnostic reagents to detect the presence or absence of thetarget DNA or RNA sequences to which they specifically bind. Suchdiagnostic tests are described in further detail below.

Likewise, the antisense constructs of the present invention, byantagonizing the normal biological activity of Ipf1 (by inhibiting itsexpression), can be used in the manipulation of tissue, e.g. tissuedifferentiation, both in vivo and in ex vivo tissue cultures, as well asin the treatment of hyperinsulinenemia, such as during various stages ofnon-insulin dependent 2) diabetes mellitus.

This invention also provides expression vectors containing a nucleicacid encoding an Ipf1 polypeptide, operably linked to at least onetranscriptional regulatory sequence. Operably linked is intended to meanthat the nucleotide sequence is linked to a regulatory sequence in amanner which allows expression of the nucleotide sequence. Regulatorysequences are art-recognized and are selected to direct expression of arecombinant Ipf1 polypeptide. Accordingly, the term transcriptionalregulatory sequence includes promoters, enhancers and other expressioncontrol elements. Such regulatory sequences are described in Goeddel;Gene Expression Technology: Methods in Enzymology 185, Academic Press,San Diego, Calif. (1990). For instance, any of a wide variety ofexpression control sequences-sequences that control the expression of aDNA sequence when operatively linked to it may be used in these vectorsto express DNA sequences encoding the Ipf1 proteins of this invention.Such useful expression control sequences, include, for example, theearly and late promoters of SV40, adenovirus or cytomegalovirusimmediate early promoter, the lac system, the trp system, the TAC or TRCsystem, T7 promoter whose expression is directed by T7 RNA polymerase,the major operator and promoter regions of phage lambda, the controlregions for fd coat protein, the promoter for 3-phosphoglycerate kinaseor other glycolytic enzymes, the promoters of acid phosphatase, e.g.,Pho5, the promoters of the yeast α-mating factors, the polyhedronpromoter of the baculovirus system and other sequences known to controlthe expression of genes of prokaryotic or eukaryotic cells or theirviruses, and various combinations thereof. It should be understood thatthe design of the expression vector may depend on such factors as thechoice of the host cell to be transformed and/or the type of proteindesired to be expressed. Moreover, the vector's copy number, the abilityto control that copy number and the expression of any other proteinsencoded by the vector, such as antibiotic markers, should also beconsidered. In one embodiment, the expression vector includes arecombinant gene encoding a polypeptide which mimics or otherwiseagonizes the action of Ipf1, or alternatively, which encodes apolypeptide that antagonizes the action of an authentic Ipf1. Suchexpression vectors can be used to transfect cells and thereby produceand (optionally) purify proteins, including fusion proteins or peptides,encoded by nucleic acids as described herein.

Moreover, the gene constructs of the present invention can also be usedas a part of a gene therapy protocol to deliver nucleic acids encodingeither an agonistic or antagonistic form of the subject Ipf1 proteins.Thus, another aspect of the invention features expression vectors for invivo transfection and expression of an Ipf1 polypeptide in particularcell types so as to reconstitute the function of, or alternatively,abrogate the function of Ipf1 in a cell in which that protein or othertranscriptional regulatory proteins to which it binds are misexpressed.For example, gene therapy can be used to deliver a gene encoding an Ipf1protein which promotes insulin expression, such as in the generation ofβ-cells.

Expression constructs of the subject Ipf1 proteins, and mutants thereof,may be administered in any biologically effective carrier, e.g. anyformulation or composition capable of effectively delivering the Ipf1gene to cells in vivo. Approaches include insertion of the subject genein viral vectors including recombinant retroviruses, adenovirus,adeno-associated virus, and herpes simplex virus-1, or recombinantbacterial or eukaryotic plasmids. Viral vectors transfect cellsdirectly; plasmid DNA can be delivered with the help of, for example,cationic liposomes (lipofectin) or derivatized (e.g. antibodyconjugated), polylysine conjugates, gramacidin S, artificial viralenvelopes or other such intracellular carriers, as well as directinjection of the gene construct or CaPO₄ precipitation carried out invivo. It will be appreciated that because transduction of appropriatetarget cells represents the critical first step in gene therapy, choiceof the particular gene delivery system will depend on such factors asthe phenotype of the intended target and the route of administration,e.g. locally or systemically. Furthermore, it will be recognized thatthe particular gene construct provided for in vivo transduction of Ipf1expression are also useful for in vitro transduction of cells. such asfor use in a diagnostic assays.

A preferred approach for in vivo introduction of nucleic acid into acell is by use of a viral vector containing nucleic acid, e.g. a cDNA,encoding the Ipf1 polypeptide or homolog thereof. Infection of cellswith a viral vector has the advantage that a large proportion of thetargeted cells can receive the nucleic acid. Additionally, moleculesencoded within the viral vector, e.g., by a cDNA contained in the viralvector, are expressed efficiently in cells which have taken up thevector.

Retrovirus vectors and adeno-associated virus vectors are generallyunderstood to be the recombinant gene delivery system of choice for thetransfer of exogenous genes in vivo, particularly into humans. Thesevectors provide efficient delivery of genes into cells, and thetransferred nucleic acids are stably integrated into the chromosomal DNAof the host. A major prerequisite for the use of retroviruses is toensure the safety of their use, particularly with regard to thepossibility of the spread of wild-type virus in the cell population. Thedevelopment of specialized cell lines (termed “packaging cells”) whichproduce only replication-defective retroviruses has increased theutility of retroviruses for gene therapy, and defective retroviruses arewell characterized for use in gene transfer for gene therapy purposes(for a review see Miller, A. D. (1990) Blood 76:271). Thus, recombinantretrovirus can be constructed in which part of the retroviral codingsequence (gag, pol, env) has been replaced by nucleic acid encoding anIpf1 polypeptide, rendering the retrovirus replication defective. Thereplication defective retrovirus is then packaged into virions which canbe used to infect a target cell through the use of a helper virus bystandard techniques. Protocols for producing recombinant retrovirusesand for infecting cells in vitro or in vivo with such viruses can befound in Current Protocols in Molecular Biology, Ausubel, F. M. et al.(eds.) Greene Publishing Associates, (1989), Sections 9.10-9.14 andother standard laboratory manuals. Examples of suitable retrovirusesinclude pLJ, pZIP, pWE and pEM which are well known to those skilled inthe art. Examples of suitable packaging virus lines for preparing bothecotropic and amphotropic retroviral systems include ψCrip, ψCre, ψ2 andψAm. Retroviruses have been used to introduce a variety of genes intomany different cell types. including epithelial cells, in vitro and/orin vivo (see for example Eglitis, et al. (1985) Science 230:1395-1398;Danos and Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:6460-6464;Wilson et al. (1988) Proc. Natl. Acad. Sci. USA 85:3014-3018; Armentanoet al. (1990) Proc. Natl. Acad. Sci. USA 87:6141-6145; Huber et al.(1991) Proc. Natl. Acad. Sci. USA 88:8039-8043; Ferry et al. (1991)Proc. Natl. Acad. Sci. USA 88:8377-8381; Chowdhury et al. (1991) Science254:1802-1805; van Beusechem et al. (1992) Proc. Natl. Acad. Sci. USA89:7640-7644; Kay et al. (1992) Human Gene Therapy 3:641-647; Dai et al.(1992) Proc. Natl. Acad Sci. USA 89:10892-10895; Hwu et al. (1993) J.Immunol. 150:4104-4115; U.S. Pat. No.: 4,868,116; U.S. Pat. No.:4,980,286; PCT Application WO 89/07136; PCT Application WO 89/02468; PCTApplication WO 89/05345; and PCT Application WO 92/07573).

Furthermore, it has been shown that it is possible to limit theinfection spectrum of retroviruses and consequently of retroviral-basedvectors, by modifying the viral packaging proteins on the surface of theviral particle (see, for example PCT publications WO93/25234 andWO94/06920). For instance, strategies for the modification of theinfection spectrum of retroviral vectors include: coupling antibodiesspecific for cell surface antigens to the viral env protein (Roux et al.(1989) PNAS 86:9079-9083; Julan et al. (1992) J. Gen Virol 73:3251-3255;and Goud et al. (1983) Virology 163:251-254); or coupling cell surfacereceptor ligands to the viral env proteins (Neda et al. (1991) J BiolChem 266:14143-14146). Coupling can be in the form of the chemicalcross-linking with a protein or other variety receptor-ligand drug, aswell as by generating fusion proteins (e.g. single-chain antibody/envfusion proteins). For example, agents which bind to β-cell receptors(either ligand or antibody) can be used to enhance infection of β-cells.To illustrate, derivatization of the viral particle with ligands for atleast one of the gluca gon-like peptide receptor (GLP), the sulfonylureareceptor, the galanin receptor, or antibodies against β-cell antigens,such as GAD65. This technique, while useful to limit or otherwise directthe infection to pancreatic tissue, can also be used to convert anecotropic vector in to an amphotropic vector.

Another viral gene delivery system useful in the present inventionutilitizes adenovirus-derived vectors. The genome of an adenovirus canbe manipulated such that it encodes and expresses a gene product ofinterest but is inactivated in terms of its ability to replicate in anormal lytic viral life cycle. See for example Berkner et al. (1988)BioTechniques 6:616; Rosenfeld et al. (1991) Science 252:431-434; andRosenfeld et al. (1992) Cell 68:143-155. Suitable adenoviral vectorsderived from the adenovirus strain Ad type 5 d1324 or other strains ofadenovirus (e.g., Ad2, Ad3, Ad7 etc.) are well known to those skilled inthe art. The virus particle is relatively stable and amenable topurification and concentration, and as above, can be modified so as toaffect the spectrum of infectivity. Additionally, introduced adenoviralDNA (and foreign DNA contained therein) is not integrated into thegenome of a host cell but remains episomal, thereby avoiding potentialproblems that can occur as a result of insertional mutagenesis insituations where introduced DNA becomes integrated into the host genome(e.g., retroviral DNA). Moreover, the carrying capacity of theadenoviral genome for foreign DNA is large (up to 8 kilobases) relativeto other gene delivery vectors (Berkner et al. cited supra; Haj-Ahmandand Graham (1986) J. Virol. 57:267). Most replication-defectiveadenoviral vectors currently in use and therefore favored by the presentinvention are deleted for all or parts of the viral E1 and E3 genes butretain as much as 80% of the adenoviral genetic material (see, e.g.,Jones et al. (1979) Cell 16:683; Berkner et al., supra; and Graham etal. in Methods in Molecular Biology, E. J. Murray, Ed. (Humana, Clifton,N.J., 1991) vol. 7. pp. 109-127). Expression of the inserted Ipf1 genecan be under control of, for example, the E1A promoter, the major latepromoter (MLP) and associated leader sequences, the E3 promoter, orexogenously added promoter sequences.

Yet another viral vector system useful for delivery of the subject Ipf1genes is the adeno-associated virus (AAV). Adeno-associated virus is anaturally occurring defective virus that requires another virus, such asan adenovirus or a herpes virus, as a helper virus for efficientreplication and a productive life cycle. (For a review see Muzyczka etal. Curr. Topics in Micro. and Immunol. (1992) 158:97-129). It is alsoone of the few viruses that may integrate its DNA into non-dividingcells, and exhibits a high frequency of stable integration (see forexample Flotte et al. (1992) Am. J. Respir. Cell. Mol. Biol. 7:349-356;Samulski et al. (1989) J. Virol. 63:3822-3828; and McLaughlin et al.(1989) J. Virol. 62:1963-1973). Vectors containing as little as 300 basepairs of AAV can be packaged and can integrate. Space for exogenous DNAis limited to about 4.5 kb. An AAV vector such as that described inTratschin et al. (1985) Mol. Cell. Biol. 5:3251-3260 can be used tointroduce Ipf1 genes into cells. A variety of nucleic acids have beenintroduced into different cell types using AAV vectors (see for exampleHermonat et al. (1984) Proc. Natl. Acad. Sci. USA 81:6466-6470;Tratschin et al. (1985) Mol. Cell. Biol. 4:2072-2081; Wondisford et al.(1988) Mol. Endocrinol. 2:32-39; Tratschin et al. (1984) J. Virol.51:611-619; and Flotte et al. (1993) J. Biol. Chem. 268:3781-3790).

In addition to viral transfer methods, such as those illustrated above,non-viral methods can also be employed to cause expression of an Ipf1polypeptide in the tissue of an animal. Most nonviral methods of genetransfer rely on normal mechanisms used by mammalian cells for theuptake and intracellular transport of macromolecules. In preferredembodiments, non-viral gene delivery systems of the present inventionrely on endocytic pathways for the uptake of the subject Ipf1 gene bythe targeted cell. Exemplary gene delivery systems of this type includeliposomal derived systems, poly-lysine conjugates, and artificial viralenvelopes.

In a representative embodiment, a therapeutic Ipf1 gene can be entrappedin liposomes bearing positive charges on their surface (e.g.,lipofectins) and (optionally) which are tagged with antibodies orligands for pancreatic cell surface antigens (Mizuno et al. (1992) NoShinkei Geka 20:547-551; PCT publication WO91/06309; Japanese patentapplication 1047381; and European patent publication EP-A-43075). Forexample, lipofection of β-cells can be carried out using liposomestagged with monoclonal antibodies against, for example, the GAD65antigen, or any other cell surface antigen present on these pancreaticcells. Alternatively, liposomes can be derivatize with such receptorligands glimepiride, glibenclamide or other sulfonylurea drug.

In clinical settings, the gene delivery systems for therapeutic Ipf1genes can be introduced into a patient (or non-human animal) by any of anumber of methods, each of which is familiar in the art. For instance, apharmaceutical preparation of the gene delivery system can be introducedsystemically, e.g. by intravenous injection, and specific transductionof the protein in the target cells occurs predominantly from specificityof transfection provided by the gene delivery vehicle, cell-type ortissue-type expression due to the transcriptional regulatory sequencescontrolling expression of the receptor gene, or a combination thereof.In other embodiments, initial delivery of the recombinant gene is morelimited with introduction into the animal being quite localized. Forexample, the gene delivery vehicle can be introduced into the pancreasby catheter (see U.S. Pat. No. 5,328,470), by stereotactic injection(e.g. Chen et al. (1994) PNAS 91: 3054-3057), or by electroporationduring a partial pancreatectomy (Dev et al. ((1994) Cancer Treat Rev20:105-115).

The pharmaceutical preparation of the gene therapy construct can consistessentially of the gene delivery system in an acceptable diluent, or cancomprise a slow release matrix in which the gene delivery vehicle isimbedded. Alternatively, where the complete gene delivery system can beproduced in tact from recombinant cells, e.g. retroviral vectors, thepharmaceutical preparation can comprise one or more cells which producethe gene delivery system.

There are a wide variety of pathological cell proliferative anddifferentiative conditions for which the Ipf1 gene constructs of thepresent invention may provide therapeutic benefits, with the generalstrategy being, for example, the correction of abherent insulinexpression, or modulation of differentiative events mediated by Ipf1,such as may be influenced by transcriptional regulatory sequences ofother genes with which the subject Ipf1 interact. More generally,however, the present invention relates to a method of inducing and/ormaintaining a differentiated state, enhancing survival and/or affectingproliferation of a cell in which Ipf1 responsive genes are expressed, bycontacting the cell with an agent which modulates the function (as anagonist or an antagonist) of Ipf1. For instance, it is contemplated bythe invention that, in light of the apparent involvement of Ipf1 in theformation of ordered spatial arrangements of pancreatic tissues, thesubject method could be used to generate and/or maintain such tissueboth in vitro and in vivo. For instance, modulation of the function ofIpf1 can be employed in both cell culture and therapeutic methodsinvolving generation and maintenance β-cells and possibly also fornon-pancreatic tissue, such as in controlling the development andmaintenance of tissue from the digestive tract, spleen, lungs, and otherorgans which derive from the primitive gut. The agent can be, asappropriate, any of the preparations described herein, including genetherapy constructs, antisense molecules, peptidomimetics or other agentsidentified in the drug screening assays provided herein.

In an exemplary embodiment, the present method can be used in thetreatment of hyperplastic and neoplastic disorders effecting pancreatictissue, particularly those characterized byabherent proliferation ofβ-cells, or mis-expression of Ipf1 or other proteins involved inregulatory complexes involving Ipf1. For instance, pancreatic cancersare marked by abnormal proliferation of pancreatic cells which canresult in alterations of insulin secretory capacity of the pancreas. Forinstance, certain pancreatic hyperplasias, such as pancreaticcarcinomas, can result in hypoinsulinemia due to dysfunction of β-cellsor decreased islet cell mass. Stimulation of Ipf1-mediated expression ofinsulin, such as by overexpression of exogenous Ipf1 in β-cells, can beused to increase the insulin production of normal β-cells in the tissue,as well as enhznce regeneration of the tissue after anti-tumor therapy.

In contrast, other pancreatic tumors, such as islet tumors (e.g.,insulinomas), are marked by overproduction of insulin (i.e.,hyperinsulinemia), which can cause hypoglycemic conditions in a patient.Indeed, hypoglycemia can result from any one of a number of differentdisorders which result in raised plasma insulin levels, including otherβ-cell abnormalities, as well as endocrinopathies, sepsis (includingmalaria), congestive cardiac failure, hepatic and renal insufficiencies,various genetic abnormalities of metabolism, and exogenous toxins (suchas alcohol). According to the present invention, hypoglycemic conditionscan be treated by administering therapeutic amounts of an agent able toantagonize Ipf1-mediated expression of insulin. Depending on the desiredhalf-life of the effects of the treatment, such agents can range frompeptidomimetic and other small molecule inhibitors of Ipf1 function, toantisense constructs, to transient or long-term gene therapy regimens.

Furthermore, the subject method can be used as part of treatments forvarious forms of diabetes, as well as other pathologies resulting fromdirect physical/chemical damage to β-cells which result in necrosis andloss of functional islet tissue. In diabetes mellitus, insulin secretionis either completely absent (IDDM) or inappropriately regulated (NIDDM).However, each is characterized by the presence of chronically elevatedlevels of blood glucose (hyperglycemia). The primary aim of treatment inboth forms is the same, namely, the reduction of blood glucose levels toas near as normal as possible. For example, treatment of IDDM typicallyinvolves administration of replacement doses of insulin. In constrast,initial therapy for NIDDM may be based in part on therapies whichinclude administration of hypoglycemic agents such as sulfonylurea,though insulin treatment in later stages of the disease may be requiredto effect normoglycemia. Accordingly, the present method can provide ameans for controlling diabetogenous glycemic levels, by administerationof an Ipf1 agonist (e.g. a hyperglycemic agent) as, for example, bycausing recombinant expression of a wild-type form of the protein inβ-islet cells of the patient, or alternatively, admininstration of anIpf1 antagonist (e.g. a hypoglycemic agent) such as a molecule whichinhibits response element binding and/or activation of insulin genetranscription by Ipf1 or Ipf1-containing complexes.

Moreover, manipulation of Ipf1-mediated gene expression, such as of theinsulin gene, may be useful for reshaping/repairing pancreatic tissueboth in vivo and in vitro. In one embodiment, the present inventionmakes use of the apparent involvement of the subject Ipf1 protein inregulating the development of pancreatic tissue responsible forformation of β-cells, e.g. induction of β-cell differentiation fromductal tissue, as well as other tissue from the lungs and other organswhich derive from the primitive gut. For example, therapeuticcompositions for modulating the role of Ipf1 in tissue differentiationcan be utilized to preserve any β-cells that have not been destroyed bydiabetic or tumorogenic causes, as well as to induce regeneration ofβ-cells so as to increase the islet mass. In general, the subject methodcan be employed therapeutically to regulate the pancreas after physical,chemical or pathological insult.

In yet another embodiment, the subject method can be applied to to cellculture techniques, and in particular, may be employed to enhance theinitial generation of prosthetic pancreatic tissue devices. Manipulationof Ipf1 function, for example, by altering the ability of the protein totransactivate Ipf1 responsive genes, can provide a means for morecarefully controlling the characteristics of a cultured tissue. In anexemplary embodiment, the subject method can be used to augmentproduction of prosthetic devices which require β-islet cells, such asmay be used in the encapsulation devices described in, for example, theAebischer et al. U.S. Pat. No. 4,892,538, the Aebischer et al. U.S. Pat.No. 5,106,627, the Lim U.S. Pat. No. 4,391,909, and the Sefton U.S. Pat.No. 4,353,888. Early progenitor cells to the pancreatic islets aremultipotential, and apparently coactive all the islet-specific genesfrom the time they first appear. As development proceeds, expression ofislet-specific hormones, such as insulin, becomes restricted to thepattern of expression characteristic of mature islet cells. Thephenotype of mature islet cells, however, is not stable in culture, asreappearence of embyonal traits in mature β-cells can be observed. Byutilizing agents which potentiate the action of Ipf1, such as Ipf1 geneexpression vectors.

Furthermore, manipulation of the differentiative state of pancreatictissue can be utilized in conjunction with transplantation of artificialpancreas so as to promote implantation, vascularization, and in vivodifferentiation and maintenance of the engrafted tissue. For instance,manipulation of Ipf1 function to affect tissue differentiation can beutilized as a means of maintaining graft viability.

As set out above, the present method is also applicable to cell culturetechniques. In one embodiment, manipulation of differentiative states ofrenal or urogenital tissue can be performed in order to provide cellslines, especially primary cell lines, which maintain a particularphenotype, such as cell lines which are derived from uteric bud cells.In another embodiment, the differentiation of gondal tissue in culture,such as Sertoli cells, can be controlled by manipulation of the subjectIpf1.

Conversely, control of one or more of the functions of Ipf1 can beaccomplished to inhibit differentiation along certain pathways,particularly where uncommitted pluripotent stem cells are beingcultured, so that cultures can be manipulated along alternatedevelopmental pathways. Accordingly, manipulation of Ipf1 function bythe present method to culture stem cells can be to inducedifferentiation of the uncommitted progenitor and thereby give rise to acommitted progenitor cell, or to cause further restriction of thedevelopmental fate of a committed progenitor cell towards becoming aterminally-differentiated neuronal cell. Such neuronal cultures can beused as convenient assay systems as well as sources of implantable cellsfor therapeutic treatments.

The manipulation of the biological function of the subject Ipf1 can becarried out using solely such reagents as described herein, or incombination with treatment with neurotrophic factors which act to moreparticularly enhance a specific differentiation fate of the neuronalprogenitor cell. In the later instance, manipulation of Ipf1 involvementin cell regulation might be viewed as ensuring that the treated cell ispoised along a certain developmental pathway so as to be properlyinduced upon contact with a neurotrophic factor.

Another aspect of the present invention concerns recombinant forms ofthe subject Ipf1 polypeptides. The term “recombinant protein” refers toa protein of the present invention which is produced by recombinant DNAtechniques, wherein generally DNA encoding the subject Ipf1 protein isinserted into a suitable expression vector which is in turn used totransform a host cell to produce the heterologous protein. Moreover, thephrase “derived from”, with respect to a recombinant gene, is meant toinclude within the meaning of “recombinant protein” those proteinshaving an amino acid sequence of a native Ipf1, or an amino acidsequence similar thereto which is generated by mutations includingsubstitutions and deletions (including truncation). Recombinant proteinspreferred by the present invention, in addition to native Ipf1, are atleast 60% homologous, more preferably 70% homologous and most preferably80% homologous with an amino acid sequence shown in one of SEQ ID No: 2.Polypeptides having an activity of the subject Ipf1 polypeptides (i.e.either agonistic or antagonistic of the naturally-occurring protein) andhaving at least about 90%, more preferably at least about 95%, and mostpreferably at least about 98-99% homology with a sequence of either inSEQ ID No: 2 are also within the scope of the invention.

The present invention further pertains to recombinant forms of thesubject Ipf1 which are evolutionarily related to the Ipf1 proteinrepresented in SEQ ID No: 2, that is, not identical, yet which arecapable of functioning as an agonist or an antagonist of at least onebiological activity of that protein. The term “evolutionarily relatedto”, with respect to amino acid sequences of recombinant Ipf1, refers toproteins which have amino acid sequences that have arisen naturally, aswell as to mutational variants which are derived, for example, byrecombinant mutagenesis. Such evolutionarily derived Ipf1 preferred bythe present invention are at least 60% homologous, more preferably 70%homologous and most preferably 80% homologous with the amino acidsequence shown in SEQ ID No: 2. Polypeptides having at least about 90%,more preferably at least about 95%, and most preferably at least about98-99% homology with a sequence shown in SEQ ID No: 2 are also withinthe scope of the invention.

The present invention further pertains to methods of producing thesubject Ipf1 polypeptides. For example, a host cell transfected with anucleic acid vector directing expression of Ipf1 can be cultured underappropriate conditions to allow expression of the polypeptide to occur.The polypeptide may be secreted, e.g. with the use of an exogenoussignal sequence, and isolated from a mixture of cells and mediumcontaining the recombinant protein. Alternatively, the peptide may beretained cytoplasmically, as the naturally occurring form of the proteinis believed to be, and the cells harvested, lysed and the proteinisolated. A cell culture includes host cells, media and otherbyproducts. Suitable media for cell culture are well known in the art.The recombinant Ipf1 polypeptide can be isolated from cell culturemedium, host cells, or both using techniques known in the art forpurifying proteins including ion-exchange chromatography, gel filtrationchromatography, ultrafiltration, electrophoresis, and immunoaffinitypurification with antibodies specific for such peptide. In a preferredembodiment, the recombinant Ipf1 is a fusion protein containing a domainwhich facilitates its purification, such as a glutathione-S-transferasedomain or a polyhistidine leader sequence in the form of a fusionprotein with the subject polypeptides.

This invention also pertains to a host cell transfected with an Ipf1gene in order to cause expression of a recombinant form of Ipf1. Thehost cell may be any prokaryotic or eukaryotic cell. Thus, a nucleotidesequence derived from the cloning of the Ipf1 encoding all or a selectedportion of the protein, can be used to produce a recombinant form ofIpf1 via microbial or eukaryotic cellular processes. Ligating apolynucleotide sequence into a gene construct, such as an expressionvector, and transforming or transfecting host cells with the vector arestandard procedures used in producing other well-known proteins, e.g.insulin, interferons, myc, p53, fos, jun, cyclins, Ikaros, and the like.Similar procedures, or modifications thereof, can be employed to preparerecombinant Ipf1, or portions thereof, by microbial means ortissue-culture technology in accord with the subject invention. Hostcells suitable for expression of recombinant Ipf1 polypeptides can beselected, for example, from amongst eukaryotic (yeast, avian, insect ormammalian) or prokaryotic (bacterial) cells.

The recombinant Ipf1 gene can be produced by ligating nucleic acidencoding a Ipf1, or a portion thereof, into a vector suitable forexpression in either prokaryotic cells, eukaryotic cells, or both.Expression vectors for production of recombinant forms of Ipf1 includeplasmids and other vectors. For instance, suitable vectors for theexpression of Ipf1 include plasmids of the types: pBR322-derivedplasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derivedplasmids and pUC-derived plasmids for expression in prokaryotic cells,such as E. coli.

A number of vectors exist for the expression of recombinant proteins inyeast. For instance, YEP24, YIP5, YEP51, YEP52, pYES2, and YRP17 arecloning and expression vehicles useful in the introduction of geneticconstructs into S. cerevisiae (see, for example, Broach et al. (1983) inExperimental Manipulation of Gene Expression, ed. M. Inouye AcademicPress, p. 83, incorporated by reference herein). These vectors canreplicate in E. coli due the presence of the pBR322 ori, and in S.cerevisiae due to the replication determinant of the yeast 2 micronplasmid. In addition, drug resistance markers such as ampicillin can beused.

Preferred mammalian expression vectors contain prokaryotic sequences tofacilitate the propagation of the vector in bacteria, and one or moreeukaryotic transcription regulatory sequences that cause expression of arecombinant Ipf1 gene in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo,pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7,pko-neo and pHyg derived vectors are examples of mammalian expressionvectors suitable for transfection of eukaryotic cells. Some of thesevectors are modified with sequences from bacterial plasmids, such aspBR322, to facilitate replication and drug resistance selection in bothprokaryotic and eukaryotic cells. Alternatively, derivatives of virusessuch as the bovine papilloma virus (BPV-1), or Epstein-Barr virus(pHEBo, pREP-derived and p205) can be used for transient expression ofproteins in eukaryotic cells. Examples of other viral (includingretroviral) expression systems can be found above in the description ofgene therapy delivery systems.

In some instances, it may be desirable to express a recombinant Ipf1 bythe use of a baculovirus expression system (see, for example, CurrentProtocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons:1992). Examples of such baculovirus expression systems includepVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derivedvectors (such as pAcUW1), and pBlueBac-derived vectors (such as theβ-gal containing pBlueBac III).

The various methods employed in the preparation of the plasmids andtransformation of host organisms are well known in the art. For othersuitable expression systems for both prokaryotic and eukaryotic cells,as well as general recombinant procedures, see Molecular Cloning ALaboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (ColdSpring Harbor Laboratory Press: 1989) Chapters 16 and 17.

When expression of a portion of one an Ipf1 protein is desired, i.e. atrunction mutant, it may be necessary to add a start codon (ATG) to theoligonucleotide fragment containing the desired sequence to beexpressed. It is well known in the art that a methionine at theN-terminal position can be enzymatically cleaved by the use of theenzyme methionine aminopeptidase (MAP). MAP has been cloned from E. coli(Ben-Bassat et al. (1987) J. Bacteriol. 169:751-XX57) and Salmonellatyphimurium and its in vitro activity has been demonstrated onrecombinant proteins (Miller et al. (1987) PNAS 84:2718-1722).Therefore, removal of an N-terminal methionine, if desired, can beachieved either in vivo by expressing Ipf1-derived polypeptides in ahost which produces MAP (e.g., E. coli or CM89 or S. cerevisiae), or invitro by use of purified MAP (e.g., procedure of Miller et al., supra).

Alternatively, the coding sequences for the polypeptide can beincorporated as a part of a fusion gene. This type of expression systemcan be useful under conditions where it is desirable to produce animmunogenic fragment of an Ipf1 protein. For example, the VP6 capsidprotein of rotavirus can be used as an immunologic carrier protein forportions of the Ipf1 polypeptide, either in the monomeric form or in theform of a viral particle. The nucleic acid sequences corresponding tothe portion of Ipf1 to which antibodies are to be raised can beincorporated into a fusion gene construct which includes codingsequences for a late vaccinia virus structural protein to produce a setof recombinant viruses expressing fusion proteins comprising a portionof the protein Ipf1 as part of the virion. It has been demonstrated withthe use of immunogenic fusion proteins utilizing the Hepatitis B surfaceantigen fusion proteins that recombinant Hepatitis B virions can beutilized in this role as well. Similarly, chimeric constructs coding forfusion proteins containing a portion of Ipf1 and the poliovirus capsidprotein can be created to enhance immunogenicity of the set ofpolypeptide antigens (see, for example, EP Publication No: 0259149; andEvans et al. (1989) Nature 339:385; Huang et al. (1988) J. Virol.62:3855; and Schlienger et al. (1992) J. Virol. 66:2).

The Multiple Antigen Peptide system for peptide-based immunization canalso be utilized to generate an immunogen, wherein a desired portion ofIpf1 is obtained directly from organo-chemical synthesis of the peptideonto an oligomeric branching lysine core (see, for example, Posnett etal. (1988) JBC 263:1719 and Nardelli et al. (1992) J. Immunol. 148:914).Antigenic determinants of the subject Ipf1-binding proteins can also beexpressed and presented by bacterial cells.

In addition to utilizing fusion proteins to enhance immunogenicity, itis widely appreciated that fusion proteins can also facilitate theexpression and purification of proteins, such the Ipf1 polypeptides ofthe present invention. For example, Ipf1 can be generated is aglutathione-S-transferase (GST) fusion protein. Such GST fusion proteinscan simplify purification of the recombinant protein, as for example, byaffinity pruification using glutathione-derivatized matrices (see, forexample, Current Protocols in Molecular Biology, eds. Ausabel et al.(N.Y.: John Wiley & Sons, 1991)). In another embodiment, a fusion genecoding for a purification leader sequence, such as a peptide leadersequence comprising a poly-(His)/enterokinase cleavage sequence, can beadded to the N-terminus of the desired portion of an Ipf1 polypeptide inorder to permit purification of the poly(His)-fusion protein by affinitychromatography using a Ni²⁺ metal resin. The purification leadersequence can then be subsequently removed by treatment with enterokinase(e.g., see Hochuli et al. (1987) J. Chromatography 411:177; andJanknecht et al. PNAS 88:8972).

Techniques for making fusion genes are known to those skilled in theart. Essentially, the joining of various DNA fragments coding fordifferent polypeptide sequences is performed in accordance withconventional techniques, employing blunt-ended or stagger-ended terminifor ligation, restriction enzyme digestion to provide for appropriatetermini, filling-in of cohesive ends as appropriate, alkalinephosphatase treatment to avoid undesirable joining, and enzymaticligation. In another embodiment, the fusion gene can be synthesized byconventional techniques including automated DNA synthesizers.Alternatively, PCR amplification of gene fragments can be carried outusing anchor primers which give rise to complementary overhangs betweentwo consecutive gene fragments which are subsequently annealed togenerate a chimeric gene sequence (see, for example, Current Protocolsin Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992).

The present invention also makes available isolated Ipf1 polypeptideswhich are isolated from, or otherwise substantially free of othercellular proteins, especially IEF1, IEF2, Is1-1 or other transcriptionalregulatory factors which might be associated with Ipf1 or which bindnucleic acid containing Ipf1-responsive elements. The term“substantially free of other cellular or viral proteins” (also referredto herein as “contaminating proteins”) or “substantially pure orpurified preparations” are defined as encompassing preparations of Ipf1polypeptides having less than 20% (by dry weight) contaminating protein,and preferably having less than 5% contaminating protein. Functionalforms of the subject Ipf1 polypeptides can be prepared, for the firsttime, as purified preparations by providing recombinant proteins asdescribed herein. By “purified”, it is meant, when referring to apolypeptide or DNA or RNA sequence, that the indicated molecule ispresent in the substantial absence of other biological macromolecules,such as other proteins (particularly transcriptional factors, as well asother contaminating proteins). The term “purified” as used hereinpreferably means at least 80% by dry weight, more preferably in therange of 95-99% by weight, and most preferably at least 99.8% by weight,of biological macromolecules of the same type present (but water,buffers, and other small molecules, especially molecules having amolecular weight of less than 5000, can be present). The term “pure” asused herein preferably has the same numerical limits as “purified”immediately above. “Isolated” and “purified” do not encompass eithernatural materials in their native state or natural materials that havebeen separated into components (e.g., in an acrylamide gel) but notobtained either as pure (e.g. lacking contaminating proteins, orchromatography reagents such as denaturing agents and polymers, e.g.acrylamide or agarose) substances or solutions. Moreover, in theinstance of purified Ipf1, the protein preparation lacks anycontaminating nucleic acids, especially nucleic acid comprising a P1promoter sequence.

Furthermore, isolated peptidyl portions of full length forms of Ipf1proteins can also be obtained by screening peptides recombinantlyproduced from the corresponding fragment of the nucleic acid encodingsuch peptides. In addition, fragments can be chemically synthesizedusing techniques known in the art such as conventional Merrifield solidphase f-Moc or t-Boc chemistry. Accordingly, DNA binding motifs (e.g.presumably inlcuding the homeodomain region) and activation domainswhich recruit other transcriptional factors (e.g. as may exist in theN-terminal fragment) can be refined to minimal sequences. For example,an Ipf1 protein may be arbitrarily divided into fragments of desiredlength with no overlap of the fragments, or preferably divided intooverlapping fragments of a desired length. The fragments can be produced(recombinantly or by chemical synthesis) and tested to identify thosepeptidyl fragments which can function as either agonists or antagonistsof wild-type Ipf1 activity, such as by microinjection assays or in vitroprotein or DNA binding assays. In an illustrative embodiment, peptidylportions of Ipf1, such as derived from the amino terminal half of theprotein or from the C-terminal portion, can tested for their ability toinhibit authentic Ipf1 activity by expression as thioredoxin fusionproteins, each of which contains a discrete fragment of the Ipf1 (see,for example, U.S. Pat. Nos. 5,270,181 and 5,292,646; and PCT publicationWO94/02502, as well the THIOFUSION kit of Invitrogen Inc, San Diego).Such fusion proteins can be utilized in the drug screening assaysdescribed below, and, if desired, peptidyl portions which areantagnositc can be synthesized as non-peptide analogs (e.g.,peptidomimetics).

It will also be possible to modify the structure of an Ipf1 polypeptidefor such purposes as enhancing therapeutic or prophylactic efficacy, orstability (e.g., ex vivo shelf life and resistance to proteolyticdegradation in vivo). Such modified peptides, when designed to retain atleast one activity of the naturally-occurring form of the protein, areconsidered functional equivalents of the Ipf1 polypeptides described inmore detail herein. Such modified peptide can be produced, for instance,by amino acid substitution, deletion, or addition.

For example, it is reasonable to expect that an isolated replacement ofa leucine with an isoleucine or valine, an aspartate with a glutamate, athreonine with a serine, or a similar replacement of an amino acid witha structurally related amino acid (i.e. conservative mutations) will nothave a major effect on the folding of the protein, and may or may nothave much of an effect on the biological activity of the resultingmolecule. Conservative replacements are those that take place within afamily of amino acids that are related in their side chains. Geneticallyencoded amino acids are can be divided into four families: (1)acidic=aspartate, glutamate; (2) basic=lysine, arginine, histidine; (3)nonpolar=alanine, valine, leucine, isoleucine, proline, phenylalanine,methionine, tryptophan; and (4) uncharged polar=glycine, asparagine,glutamine, cysteine, serine, threonine, tyrosine. Phenylalanine,tryptophan, and tyrosine are sometimes classified jointly as aromaticamino acids. In similar fashion, the amino acid repertoire can begrouped as (1) acidic=aspartate, glutamate; (2) basic=lysine, argininehistidine, (3) aliphatic=glycine, alanine, valine, leucine, isoleucine,serine, threonine, with serine and threonine optionally be groupedseparately as aliphatichydroxyl; (4) aromatic=phenylalanine, tyrosine,tryptophan; (5) amide=asparagine, glutamine; and (6)sulfur-containing=cysteine and methionine (see, for example,Biochemistry, 2nd ed., Ed. by L. Stryer, WH Freeman and Co.: 1981).Alternatively, amino acid replacement can be based on steric criteria,e.g. isosteric replacements, without regard for polarity or charge ofamino acid sidechains. Whether a change in the amino acid sequence of apolypeptide results in a functional Ipf1 homolog (e.g. functional in thesense that it acts to mimic or antagonize the wild-type form) can bereadily determined by assessing the ability of the variant peptide toproduce a response in cells in a fashion similar to the wild-type Ipf1protein or competitively inhibit such a response. Peptides in which morethan one replacement has taken place can readily be tested in the samemanner.

This invention further contemplates a method of generating sets ofcombinatorial mutants of Ipf1, as well as truncation and fragmentationmutants, and is especially useful for identifying potential variantsequences (e.g. Ipf1 homologs) which are functional in Ipf1-dependenttranscriptional activation, but differ from a wild-type form of theprotein by, for instance, efficacy, potency and/or intracellularhalf-life. One purpose for screening such combinatorial libraries is,for example, to isolate novel Ipf1 homologs which function as either anagonist or an antagonist of the biological activities of the wild-typeprotein, or alternatively, possess novel activities all together. Toillustrate, Ipf1 homologs can be engineered by the present method toprovide proteins which bind to Ipf1-responsive elements yet preventcomplete assembly of Ipf1-dependent transcription regulatory complexes.Such proteins, when expressed from recombinant DNA constructs, can beused in gene therapy protocols as Ipf1 antagonists.

Likewise, mutagenesis can give rise to Ipf1 homologs which haveintracellular half-lives dramatically different than the correspondingwild-type protein. For example, the altered protein can be renderedeither more stable or less stable to proteolytic degradation or othercellular process which result in destruction of, or otherwiseinactivation of, the naturally-occurring forms of Ipf1. Such Ipf1homologs, and the genes which encode them, can be utilized to alter theenvelope of expression for a particular recombinant Ipf1 by modulatingthe half-life of the recombinant protein. For instance, a shorthalf-life can give rise to more transient biological effects associatedwith a particular recombinant Ipf1 protein and, when part of aninducible expression system, can allow tighter control of recombinantprotein levels within a cell. As above, such proteins, and particularlytheir recombinant nucleic acid constructs, can be used in gene therapyprotocols.

In an illustrative embodiment of this method, the amino acid sequencesfor a population of Ipf1 homologs or other related proteins are aligned,preferably to promote the highest homology possible. Such a populationof variants can include, for example, Ipf1 homologs from one or morespecies (e.g. orthologs), or Ipf1 homologs from the same species butwhich differ due to mutation, and other proteins related in some way toIpf1. Amino acids which appear at each position of the aligned sequencesare selected to create a degenerate set of combinatorial sequences.There are many ways by which the library of potential Ipf1 homologs canbe generated from a degenerate oligonucleotide sequence. Chemicalsynthesis of a degenerate gene sequence can be carried out in anautomatic DNA synthesizer, and the synthetic genes then be ligated intoan appropriate gene for expression. The purpose of a degenerate set ofgenes is to provide, in one mixture, all of the sequences encoding thedesired set of potential Ipf1 sequences. The synthesis of degenerateoligonucleotides is well known in the art (see for example, Narang, S A(1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rdCleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam: Elsevierpp. 273-289. Itakura et al. (1984) Annu. Rev. Biochem. 53.323; Itakuraet al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res.11:477. Such techniques have been employed in the directed evolution ofother proteins (see, for example, Scott et al. (1990) Science249:386-390; Roberts et al. (1992) PNAS 89:2429-2433; Devlin et al.(1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87: 6378-6382; aswell as U.S. Pat. Nos.: 5,223,409, 5,198,346, and 5,096,815).

Alternatively, other forms of mutagenesis can be utilized to generate acombinatorial library. For example, Ipf1 homologs (both agonist andantagonist forms) can be generated and isolated from a library byscreening using, for example, alanine scanning mutagenesis and the like(Ruf et al. (1994) Biochemistry 33:15 65-1572; Wang et al. (1994) J.Biol. Chem. 269:3095-3099; Balint et al. (1993) Gene 137:109-118;Grodberg et al. (1993) Eur. J. Biochem. 218:597-601; Nagashima et al.(1993) J. Biol. Chem. 268:2888-2892; Lowinan et al. (1991) Biochemistry30:10832-10838; and Cunningham et al. (1989) Science 244:1081-1085), bylinker scanning mutagenesis (Gustin et al. (1993) Virology 193:653-660;Brown et al. (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al. (1982)Science 232:316); by saturation mutagenesis (Meyers et al. (1986)Science 232:613); by PCR mutagenesis (Leung et al. (1989) Method CellMol Biol 1:11-19); or by random mutagenesis (Miller et al. (1992) AShort Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor,N.Y.; and Greener et al. (1994) Strategies in Mol Biol 7:32-34).

A wide range of techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations, as well asfor screening cDNA libraries for gene products having a certainproperty. Such techniques will be generally adaptable for rapidscreening of the gene libraries generated by the combinatorialmutagenesis of Ipf1. The most widely used techniques for screening largegene libraries typically comprises cloning the gene library intoreplicable expression vectors, transforming appropriate cells with theresulting library of vectors, and expressing the combinatorial genesunder conditions in which detection of a desired activity facilitatesrelatively easy isolation of the vector encoding the gene whose productwas detected. The illustrative assays described below are amenable tohigh through-put analysis as necessary to screen large numbers ofdegenerate Ipf1 sequences created by combinatorial mutagenesistechniques.

In one screening assay, the candidate gene products are expressed incells which are co-transfected within Ipf1-dependent reporter construct,such as the Ins-CAT vector described in Walker et al. (1983, Nature306:557-561). Ipf1 homologs from the library which can mimic thefunction of Ipf1 (e.g. or Ipf1 agonists) will be detected by theirability to activate expression of the reporter gene. In preferredembodiments, detection and isolation of genes encoding Ipf1 agonistsutilize a reporter construct which permits isolation of cells expressingthese genes by providing a selectable marker such as drug resistance orluminescence. For example, a reporter construct can be provided whichplaces the neo gene (provides resistance to G418 antibiotics) under thecontrol of an Ipf1-responsive element, such as multiple P1 promotersequences. Agonistic forms of Ipf1 will therefor confer resistance toG418, and permit isolation of Ipf1 clones from the library based on thatselection criteria. Alternatively, the drug resistance gene can bereplaced with a luminescence marker such as luciferase, such thatIpf1-induced expression is detected by luminescence of the cell.Accordingly, Ipf1 clones which activate expression of the luminescencemarker can be isolated from the library by, for example, sorting thetransfected cells with a fluorescence-activated cell sorter (FACS).

In similar fashion, antagonistic mutants of Ipf1 can be detected andisolated from the library based on their ability inhibit Ipf1 activationof a reporter gene. Co-transfection of cells with the constructs of theIpf1 library, wild-type Ipf1, and a reporter gene permit this inhibitoryactivity to be observed. For example, the luciferase reporter describedabove, when transfected in a cell expressing wild-type Ipf1 and an Ipf1mutant from the library, will be activated in cells wherein the Ipf1mutant is an agonist, or dysfunctional (e.g. mis-folded), but repressedwhenever an Ipf1 mutant antagonizes the function of the wild-type Ipf1protein. For instance, Ipf1 homologs can be isolated from the librarywhich the retain the ability to bind an Ipf1-responsive element, butwhich are defective for recruiting other transcriptional complexes tothe promoter site, or alternatively, which retain the ability to bindother proteins involved in Ipf1 complexes but which are defective inbinding to an Ipf1-responsive element. The reporter construct may alsobe generated with a marker gene whose expression is toxic or cytostaticto the host cell such that expression of an Ipf1 antagonist is detectedby its ability to rescue the cell through inhibition of the reportergene expression.

The invention also provides for reduction of the Ipf1 protein togenerate mimetics, e.g. peptide or non-peptide agents, which are able todisrupt binding of Ipf1 to promoter sequences or to other regulatoryproteins. Thus, such mutagenic techniques as described above are alsouseful to map the determinants of Ipf1 which participate inprotein—protein interactions involved in, for example, formingtranscriptional complexes. To illustrate, the critical residues of aIpf1 which are involved in molecular recognition of Ipf1 can bedetermined and used to generate Ipf1-derived peptidomimetics thatcompetitively inhibit binding of Ipf1 to other regulatory proteins or toIpf1-responsive elements. By employing, for example, scanningmutagenesis to map the amino acid residues of Ipf1 apparently involvedin complex formation, peptidomimetic compounds can be generated whichmimic those residues, and which, by inhibiting binding of the Ipf1 toother regulatory proteins, can interfere with the function of Ipf1 intranscriptional regulation of one or more genes. For instance,non-hydrolyzable peptide analogs of such residues can be generated usingretro-inverse peptides (e.g., see U.S. Pat. Nos. 5,116,947 and5,218,089; and Pallai et al. (1983) Int J Pept Protein Res 21:84-92)benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry andBiology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands.1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry andBiology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands,1988), substituted gama lactam rings (Garvey et al. in Peptides:Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,Netherlands, 1988), keto-methylene pseudopeptides (Ewenson et al. (1986)J Med Chem 29:295; and Ewenson et al. in Peptides: Structure andFunction (Proceedings of the 9th American Peptide Symposium) PierceChemical Co. Rockland, Ill., 1985), β-turn dipeptide cores (Nagai et al.(1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J Chem Soc PerkinTrans 1:1231), and β-aminoalcohols (Gordon et al. (1985) Biochem BiophysRes Commun126:419; and Dann et al. (1986) Biochem Biophys Res Commun134:71).

Another aspect of the invention pertains to an antibody specificallyreactive with an Ipf1 protein. For example, by using immunogens derivedfrom Ipf1, anti-protein/anti-peptide antisera or monoclonal antibodiescan be made by standard protocols (See, for example, Antibodies: ALaboratory Manual ed. by Harlow and Lane (Cold Spring Harbor Press:1988)). A mammal, such as a mouse, a hamster or rabbit can be immunizedwith an immunogenic form of the peptide (e.g., a full length Ipf1 or anantigenic fragment which is capable of eliciting an antibody response).Techniques for conferring immunogenicity on a protein or peptide includeconjugation to carriers or other techniques well known in the art. Animmunogenic portion of Ipf1 can be administered in the presence ofadjuvant. The progress of immunization can be monitored by detection ofantibody titers in plasma or serum. Standard ELISA or other immunoassayscan be used with the immunogen as antigen to assess the levels ofantibodies. In a preferred embodiment, the subject antibodies areimmunospecific for antigenic determinants of an Ipf1 protein of thepresent invention, e.g. antigenic determinants of the proteinrepresented by SEQ ID No: 2 or a closely related human or non-humanmammalian homolog thereof. For instance, a favored anti-Ipf1 antibody ofthe present invention does not substantially cross react (i.e. reactspecifically) with a protein which is less than 90 percent homologous toSEQ ID No: 2; though antibodies which do not substantially cross reactwith a protein which is less than 95 percent homologous with SEQ ID No:2, or even less than 98-99 percent homologous with SEQ ID No: 2, arespecifically contemplated. By “not substantially cross react”, it ismeant that the antibody has a binding affinity for a non-homologousprotein (e.g. other insulin promoter-binding proteins such as IEF2, aswell as other homeobox proteins which do not bind the insulin promoter)which is at least one order of magnitude, more preferably at least twoorders of magnitude and even more preferably at least 3 orders ofmagnitude less than the binding affinity for a protein represented bySEQ ID No: 2.

Following immunization, anti-Ipf1 antisera can be obtained and, ifdesired, polyclonal anti-Ipf1 antibodies isolated from the serum. Toproduce monoclonal antibodies, antibody producing cells (lymphocytes)can be harvested from an immunized animal and fused by standard somaticcell fusion procedures with immortalizing cells such as myeloma cells toyield hybridoma cells. Such techniques are well known in the art, aninclude, for example, the hybridoma technique (originally developed byKohler and Milstein, (1975) Nature, 256: 495-497), the human B cellhybridoma technique (Kozbar et al., (1983) Immunology Today, 4: 72), andthe EBV-hybridoma technique to produce human monoclonal antibodies (Coleet al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss,Inc. pp. 77-96). Hybridoma cells can be screened immunochemically forproduction of antibodies specifically reactive with a Ipf1 of thepresent invention and monoclonal antibodies isolated from a culturecomprising such hybridoma cells.

The term antibody as used herein is intended to include fragmentsthereof which are also specifically reactive with an Ipf1 protein.Antibodies can be fragmented using conventional techniques, includingrecombinant engineering, and the fragments screened for utility in thesame manner as described above for whole antibodies. For example,F(ab′)₂ fragments can be generated by treating antibody with pepsin. Theresulting F(ab′)₂ fragment can be treated to reduce disulfide bridges toproduce Fab′ fragments. The antibody of the present invention is furtherintended to include bispecific and chimeric molecules having ananti-Ipf1 portion.

Both monoclonal and polyclonal antibodies (Ab) directed against an Ipf1protein can be used to block the action of that protein and allow thestudy of the role of Ipf1 in transcriptional regulation generally, or inthe etiology of β-cell development or islet cell transformation, e.g. bymicroinjection of anti-Ipf1 into cells.

Antibodies which specifically bind Ipf1 epitopes can also be used inimmunohistochemical staining of tissue samples in order to evaluate theabundance and pattern of expression of Ipf1. Anti-Ipf1 antibodies can beused diagnostically in immuno-precipitation and immuno-blotting todetect and evaluate Ipf1 levels in tissue or bodily fluid as part of aclinical testing procedure. For instance, such measurements can beuseful in predictive valuations of the onset or progression of, forexample, diabetes or other β-cell abnormalities. Likewise, the abilityto monitor Ipf1 levels in the cells of an individual can permitdetermination of the efficacy of a given treatment regimen for anindividual afflicted with such a disorder. The level of Ipf1 can bemeasured in cells found in bodily fluid, or can be measured in tissue,such as pancreatic biopsies. Diagnostic assays using anti-Ipf1antibodies can include, for example, immunoassays designed to aid inearly detection of β-cell necrosis (e.g. IDPM), or in the diagnosis of aneoplastic or hyperplastic disorder, and may aid in detecting thepresence by detecting cells in which a lesion of the Ipf1 gene hasoccurred or in which the protein is misexpressed or found in abnormalprotein complexes, or found in abnormally high levels in serum or plasmaindicating cytolysis of β-cells.

Another application of the subject antibodies is in the immunologicalscreening of cDNA libraries constructed in expression vectors such asλgt11, λgt18-23, λZAP, and λORF8. Messenger libraries of this type,having coding sequences inserted in the correct reading frame andorientation, can produce fusion proteins. For instance, λgt11 willproduce fusion proteins whose amino termini consist of β-galactosidaseamino acid sequences and whose carboxy termini consist of a foreignpolypeptide. Antigenic epitopes of an Ipf1 protein can then be detectedwith antibodies, as, for example, reacting nitrocellulose filters liftedfrom infected plates with anti-Ipf1 antibodies. Phage, scored by thisassay, can then be isolated from the infected plate. Thus, the presenceof Ipf1 homologs can be detected and cloned from other animals,including humans, and alternate isoforms (including splicing variants)can also be detected and cloned from the same species.

Moreover, the nucleotide sequence determined from the cloning of thesubject Ipf1 will further allow for the generation of probes designedfor use in identifying homologs in other cell types, as well as Ipf1homologs (e.g. orthologs) from other animals. For instance, the presentinvention also provides a probe/primer comprising a substantiallypurified oligonucleotide, which oligonucleotide comprises a region ofnucleotide sequence that hybridizes under stringent conditions to atleast 10 consecutive nucleotides of sense or anti-sense sequence of SEQID No: 1, or naturally occurring mutants thereof. In preferredembodiments, the probe/primer further comprises a label group attachedthereto and able to be detected, e.g. the label group is selected fromthe group consisting of radioisotopes, fluorescent compounds, enzymes,and enzyme co-factors. Such probes can also be used as a part of adiagnostic test kit for identifying transformed cells, such as formeasuring a level of an Ipf1 nucleic acid in a sample of cells from apatient; e.g. detecting mRNA encoding Ipf1 mRNA level or determiningwhether a genomic Ipf1 gene has been mutated or deleted.

In addition, nucleotide probes can be generated which allow forhistological screening of intact tissue and tissue samples for thepresence of an Ipf1 mRNA. Similar to the diagnostic uses of anti-Ipf1antibodies, the use of probes directed to Ipf1 mRNAs, or to genomic Ipf1sequences, can be used for both predictive and therapeutic evaluation ofallelic mutations which might be manifest in, for example, diabeticdisorders as well as neoplastic or hyperplastic disorders (e.g. unwantedcell growth) or abnormal differentiation of tissue. Used in conjunctionwith an antibody immunoassays, the nucleotide probes can help facilitatethe determination of the molecular basis for a developmental disorderwhich may involve some abnormality associated with expression (or lackthereof) of Ipf1. For instance, variation in synthesis of Ipf1 can bedistinguished from a mutation in the genes coding sequence.

Accordingly, the present method provides a method for determining if asubject is at risk for a disorder characterized by unwanted cellproliferation or abherent control of differentiation, particularly ofpancreatic tissue. In preferred embodiments, the subject method can begenerally characterized as comprising detecting, in a tissue sample ofthe subject (e.g. a human patient), the presence or absence of a geneticlesion characterized by at least one of (i) a mutation of a geneencoding Ipf1 or (ii) the mis-expression of an Ipf1 gene. To illustrate,such genetic lesions can be detected by ascertaining the existence of atleast one of (i) a deletion of one or more nucleotides from an Ipf1gene, (ii) an addition of one or more nucleotides to such an Ipf1 gene,(iii) a substitution of one or more nucleotides of an Ipf1 gene, (iv) agross chromosomal rearrangement of an Ipf1 gene, (v) a gross alterationin the level of a messenger RNA transcript of an Ipf1 gene, (vi) thepresence of a non-wild type splicing pattern of a messenger RNAtranscript of an Ipf1 gene, and (vii) a non-wild type level of an Ipf1protein. In one aspect of the invention there is provided a probe/primercomprising an oligonucleotide containing a region of nucleotide sequencewhich is capable of hybridizing to a sense or antisense sequence of SEQID No: 1, or naturally occurring mutants thereof, or 5′ or 3′ flankingsequences or intronic sequences naturally associated with the subjectIpf1 gene. The probe is exposed to nucleic acid of a tissue sample; andthe hybridization of the probe to the sample nucleic acid is detected.In certain embodiments, detection of the lesion comprises utilizing theprobe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Pat.Nos.: 4,683,195 and 4,683,202) or, alternatively, in a ligation chainreaction (LCR) (see, e.g., Landegran et al. (1988) Science,241:1077-1080; and NaKazawa et al. (1944) PNAS 91:360-364) the later ofwhich can be particularly useful for detecting point mutations in anIpf1 gene. Alternatively, immunoassays can be employed to determine thelevel of Ipf1 protein and/or its participation in protein complexes,particularly transcriptional regulatory complexes such as those whichactivate insulin expression.

Also, by inhibiting endogenous production of Ipf1, anti-sense techniques(e.g. microinjection of antisense molecules, or transfection withplasmids whose transcripts are anti-sense with regard to an Ipf1 mRNA orgene sequence) can be used to investigate the role of Ipf1 in growth anddifferentiative events, such as those giving rise to pancreaticdevelopment, as well as abnormal cellular functions in which Ipf1 mayparticipate, e.g. in mis-regulation of insulin expression. Suchtechniques can be utilized in cell culture, but can also be used in thecreation of transgenic animals.

Furthermore, by making available purified and recombinant Ipf1, thepresent invention facilitates the development of assays which can beused to screen for drugs which are either agonists or antagonists of thecellular function Ipf1, such as its role in the pathogenesis ofproliferative and differentiative disorders, as well as in insulinregulation. For instance, an assay can be generated according to thepresent invention which evaluates the ability of a compound to modulatebinding between Ipf1 and other transcriptional regulatory proteins orIpf1-responsive elements. A variety of assay formats will suffice and,in light of the present inventions, will be comprehended by skilledartisan.

In many drug screening programs which test libraries of compounds andnatural extracts, high throughput assays are desirable in order tomaximize the number of compounds surveyed in a given period of time.Assays which are performed in cell-free systems, such as may be derivedwith purified or semi-purified proteins, are often preferred as“primary” screens in that they can be generated to permit rapiddevelopment and relatively easy detection of an alteration in amolecular target when contacted with a test compound. Moreover, theeffects of cellular toxicity and/or bioavailability of the test compoundcan be generally ignored in the in vitro system, the assay instead beingfocused primarily on the effect of the drug on the molecular target asmay be manifest in an alteration of binding affinity with other proteinswith a nucleic acid. Accordingly, in an exemplary screening assay of thepresent invention, the compound of interest is contacted with a mixturegenerated from an isolated and purified Ipf1 polypeptide and a nucleicacid which specifically binds Ipf1 (e.g. Ipf1-responsive element) suchas the P1 insulin promoter. Detection and quantification ofIpf1/promoter complexes provides a means for determining the compound'sefficacy at inhibiting (or potentiating) DNA binding by Ipf1. Similarly,other regulatory proteins which are identified as binding Ipf1 can beused in place of the nucleic acid. The efficacy of the compound can beassessed by generating dose response curves from data obtained usingvarious concentrations of the test compound. Moreover, a control assaycan also be performed to provide a baseline for comparison. In thecontrol assay, isolated and purified Ipf1 is added to a compositioncontaining the nucleic acid (or the other regulatory proteins), and theformation of Ipf1-containing complexes is quantitated in the absence ofthe test compound.

The formation of complexes including Ipf1 may be detected by a varietyof techniques. For instance, modulation in the formation of complexescan be quantitated using, for example, detectably labelled proteins(e.g. radiolabelled, fluorescently labelled, or enzymatically labelled),by immunoassay, or by chromatographic detection.

Typically, it will be desirable to immobilize either the Ipf1 protein orthe DNA or other regulatory protein (hereinafter “target molecule”) tofacilitate separation of target/Ipf1 complexes from uncomplexed forms,as well as to accomadate automation of the assay. In an illustrativeembodiment, a fusion protein can be provided which adds a domain thatpermits Ipf1 to be bound to an insoluble matrix. For example,glutathione-S-transferase/Ipf1 (GST/Ipf1) fusion proteins can beadsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis,Mo.) or glutathione derivatized microtitre plates, which are thencombined with the target molecule, e.g. an ³⁵S-labeled protein or DNAfragment, and the test compound, and mixture incubated under conditionsconducive to complex formation. Following incubation, the beads arewashed to remove any unbound target molecule and the matrix bead-boundradiolabel determined directly (e.g. beads placed in scintilant), or inthe superntantant after the complexes are dissociated, e.g. whenmicrotitre plates are used. Alternatively, after washing away unboundprotein, the complexes can be dissociated from the matrix, separated bySDS-PAGE gel, and the amount of target molecules found in thematrix-bound fraction quantitated from the gel using standardelectrophoretic techniques.

Other techniques for immobilizing proteins or DNA on matrices are alsoavailable for use in the subject assay. For instance, the DNA targetprotein can be immobilized utilizing conjugation of biotin andstreptavidin. Biotinylated DNA can be prepared using techniques wellknown in the art and immobilized in the wells of streptavidin-coated 96well plates (Pierce Chemical) and Ipf1 binding to the immobilizednucleic acid detected. Exemplary methods for detecting such complexes,in addition to those described above for the GST-immobilized Ipf1complexes, include immunodetection of complexes using antibodiesreactive with Ipf1 as well as enzyme-linked assays which rely ondetecting an enzymatic activity associated with Ipf1. In the instance ofthe latter, the enzyme can be chemically conjugated or provided as afusion protein with the Ipf1 polypeptide. To illustrate, Ipf1 can bechemically cross-linked with alkaline phosphatase, and the amount ofIpf1 trapped in the complex can be assessed with a chromogenic substrateof the enzyme, e.g. paranitrophenyl phosphate. Likewise, a fusionprotein comprising the Ipf1 and glutathione-S-transferase can beprovided, and complex formation quantitated by detecting the GSTactivity using 1-chloro-2,4-dinitrobenzene (Habig et al (1974) J BiolChem 249:7130).

For processes which rely on immunodetection for quatitating Ipf1 trappedin the complex, antibodies against the protein, such as the anti-Ipf1antibodies described herein, can be used. Alternatively, the protein tobe detected in the complex can be “epitope tagged” in the form of afusion protein which includes, in addition to Ipf1 sequences, a secondpolypeptide for which antibodies are readily available (e.g. fromcommercial sources). For instance, the GST fusion proteins describedabove can also be used for quantification of binding using antibodiesagainst the GST moiety. Other useful epitope tags include myc-epitopes(e.g., see Ellison et al. (1991) J Biol Chem 266:21150-21157) whichincludes a 10-residue sequence from c-myc, as well as the pFLAG system(International Biotechnologies, Inc.) or the pEZZ-protein A system(Pharamacia, N.J.).

In another embodiment, the assay format is derived in a similar mannerto the use of Ipf1-sensitve reporter constructs described above. Forexample, co-transfection of an Ipf1-deficient cell (e.g. a COS or CHOcell) with an Ipf1 expression vector and an Ipf1-dependent reporterconstruct provides a convenient system for identifying compounds basedon their ability to affect Ipf1-dependent transcription.

Additionally, Ipf1 can be used to generate an interaction trap assay(see, U.S. Pat. No.: 5,283,317; PCT publication WO94/10300; Zervos etal. (1993) Cell 72:223-232; Madura et al. (1993) J Biol Chem268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; andIwabuchi et al. (1993) Oncogene 8:1693-1696), for detecting agents whicheither potentiate or attenuate complex formation between a Ipf1 andother transcriptional regulatory proteins. Indeed, an interaction trapassay generated with Ipf1 as a bait protein can be used to identifyother cellular proteins which bind Ipf1, and which would therefore beimplicated in Ipf1 transcriptional regulation, such as by participatingin regulatory complexes, or by causing post-translational modification(e.g. phosphenylation or ubiquitination) of Ipf1.

The interaction trap assay relies on reconstituting in vivo a functionaltranscriptional activator protein from two separate fusion proteins, oneof which comprises the DNA-binding domain of a transcriptional activatorfused to an Ipf1 polypeptide (which preferably lacks its own DNA bindingability). The second fusion protein comprises a transcriptionalactivation domain (e.g. able to initiate RNA polymerase transcription)fused to a protein which binds Ipf1. When the two fusion proteinsinteract, the two domains of the transcriptional activator protein arebrought into sufficient proximity as to cause transcription of areporter gene. In an illustrative embodiment, Saccharomyces cerevisiaeYPB2 cells are transformed simultaneously with a plasmid encoding aGAL4db-Ipf1 (Δ homeodomain) fusion (db: DNA binding domain) and with aplasmid encoding the GAL4 activation domain (GAL4ad) fused to anIpf1-binding protein, wherein Ipf1 (Δ homeodomain) designates an Ipf1mutant lacking a homeodomain able to an Ipf1-responsive ement, such asan Ipf1 in which His-190 is deleted, or wherein the protein is truncated(e.g. comprises residues 1-145). Moreover, the strain is transformedsuch that the GAL4-responsive promoter drives expression of a phenotypicmarker. For example, the ability to grow in the absence of histidine candepends on the expression of the HIS3 gene. When the HIS3 gene is placedunder the control of a GAL4-responsive promoter, relief of thisauxotrophic phenotype indicates that a functional GAL4 activator hasbeen reconstituted through the interaction of the target protein andIpf1. Thus, agents able to inhibit Ipf1 interaction with target proteinwill result in yeast cells unable to growth in the absence of histidine.Alternatively, the phenotypic marker (e.g. instead of the HIS3 gene) canbe one which provides a negative selection when expressed such thatagents which disrupt this Ipf1-dependent interaction confer positivegrowth selection to the cells. Comercial kits which can be modified todevelop two-hybrid assays with the subject Ipf1 are presently available(e.g., MATCHMAKER kit, ClonTech catalog number K1605-1, Palo Alto,Calif.). This assay can also be used to screen cDNA libraries for Ipf1interactors, by generating a library of cDNA:Ad constructs.

Another aspect of the present invention concerns transgenic animalswhich are comprised of cells (of that animal) which contain a transgeneof the present invention and which preferably (though optionally)express an exogenous Ipf1 in one or more cells in the animal. The Ipf1transgene can encode the wild-type form of the protein, or can encodehomologs thereof, including both agonists and antagonists, as well asantisense constructs designed to inhibit expression of the endogenousgene. In preferred embodiments, the expression of the transgene isrestricted to specific subsets of cells, tissues or developmental stagesutilizing, for example, cis-acting sequences that control expression inthe desired pattern. In the present invention, such mosiac expression ofthe subject Ipf1 can be essential for many forms of lineage analysis andcan additionally provide a means to assess the effects of, for example,antagonism of Ipf1 action, which deficiency might grossly alterdevelopment in small patches of tissue within an otherwise normalembryo. Toward this and, tissue-specific regulatory sequences andconditional regulatory sequences can be used to control expression ofthe transgene in certain spatial patterns. Moreover, temporal patternsof expression can be provided by, for example, conditional recombinationsystems or prokaryotic transcriptional regulatory sequences.

Genetic techniques which allow for the expression of transgenes can beregulated via site-specific genetic manipulation in vivo are known tothose skilled in the art. For instance, genetic systems are availablewhich allow for the regulated expression of a recombinase that catalyzesthe genetic recombination a target sequence. As used herein, the phrase“target sequence” refers to a nucleotide sequence that is geneticallyrecombined by a recombinase. The target sequence is flanked byrecombiriase recognition sequences and is generally either excised orinverted in cells expressing recombinase activity. Recombinase catalyzedrecombination events can be designed such that recombination of thetarget sequence results in either the activation or repression ofexpression of Ipf1 or in disruption of the coding sequence. For example,excision of a target sequence which interferes with the expression of arecombinent Ipf1 gene can be designed to activate expression of thatgene. This interference with expression of the protein can result from avariety of mechanisms, such as spatial separation of the gene from apromoter element or an internal stop codon. Moreover, the transgene canbe made wherein the coding sequence of the gene is flanked byrecombinase recognition sequences and is initially transfected intocells in a 3′ to 5′ orientation with respect to the promoter element. Insuch an instance, inversion of the target sequence will reorient thesubject gene by placing the 5′ end of the coding sequence in anorientation with respect to the promoter element which allow forpromoter driven transcriptional activation. Alternatively, recombinasesites can be placed in intronic sequence and, by homologousrecombination inserted into the genomic Ipf1 gene such that inversion ofexcisim of the target sequence inactivates the Ipf1 allele.

In an illustrative embodiment, either the cre/loxP recombinase system ofbacteriophage P1 (Lakso et al. (1992) PNAS 89:6232-6236; Orban et al.(1992) PNAS 89:6861-6865) or the FLP recombinase system of Saccharomycescerevisiae (O'Gorman et al. (1991) Science 251:1351-1355; PCTpublication WO 92/15694) can be used to generate in vivo site-specificgenetic recombination systems. Cre recombinase catalyzes thesite-specific recombination of an intervening target sequence locatedbetween loxP sequences. loxP sequences are 34 base pair nucleotiderepeat sequences to which the Cre recombinase binds and are required forCre recombinase mediated genetic recombination. The orientation of loxPsequences determines whether the intervening target sequence is excisedor inverted when Cre recombinase is present (Abremski et al. (1984) J.Biol. Chem. 259:1509-1514); catalyzing the excision of the targetsequence when the loxP sequences are oriented as direct repeats andcatalyzes inversion of the target sequence when loxP sequences areoriented as inverted repeats.

Accordingly, genetic recombination of the target sequence is dependenton expression of the Cre recombinase. Expression of the recombinase canbe regulated by promoter elements which are subject to regulatorycontrol, e.g., tissue-specific, developmental stage-specific, inducibleor repressible by externally added agents. This regulated control willresult in genetic recombination of the target sequence only in cellswhere recombinase expression is mediated by the promoter element. Thus,the activation or exogenous expression of a Ipf1, or alternatively,disruption of the endogenous Ipf1 gene, can be regulated via regulationof recombinase expression.

Use of the cre/loxP recombinase system to regulate expression of arecombinant Ipf1 gene, requires the construction of a transgenic animalcontaining transgenes encoding both the Cre recombinase and the subjectprotein. Animals containing both the Cre recombinase and the recombinantIpf1 gene can be provided through the construction of “double”transgenic animals. A convenient method for providing such animals is tomate two transgenic animals each containing a transgene, e.g., the Ipf1gene in one animal and recombinase gene in the other. Similar transgenemanipulation can be used to generate animals dependent on recombinaseexpression for disruption of the Ipf1 gene.

One advantage derived from initially constructing transgenic animalscontaining a transgene in a recombinase-mediated expressible formatderives from the likelihood that the subject protein will be deleteriousupon expression in the transgenic animal such as the pancreas deficientmice described below. In such an instance, a founder population, inwhich the subject transgene is silent in all tissues, can be propagatedand maintained. Individuals of this founder population can be crossedwith animals expressing the recombinase in, for example, one or moretissues. Thus, the creation of a founder population in which, forexample, an antagonistic Ipf1 transgene is silent will allow the studyof progeney from that founder in which disruption of Ipf1transcriptional regulatory complexes in a particular tissue or atcertain developmental stages would result in, for example, a lethalphenotype.

Similar conditional transgenes can be provided using either prokaryoticor viral promoter sequences which require prokaryotic or viral proteinsto be simultaneous expressed in the cell in order to facilitateexpression of the transgene. Exemplary promoters and the correspondingtrans-activating prokaryotic proteins are given in U.S. Pat. No.:4,833,080, and conditional viral expression systems are provided in U.S.Pat. No. 5,221,778. Moreover, expression of the conditional transgenescan be induced by gene therapy-like methods wherein a gene encoding thetrans-activating protein, e.g. a recombinase or a prokaryotic protein,is delivered to the tissue and caused to be expressed using, forexample, one of the gene therapy constructs described above. By thismethod, the Ipf1 transgene could remain silent into adulthood and itsexpression “turned on” by the introduction of the trans-activator.

Methods of making transgenic animals are well known in the art. Forexample, see Manipulating the Mouse Embryo, (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1986), and U.S. Pat. Nos.5,347,075; 5,322,775; 5,221,778; 5,175,385; 5,175,384; 5,175,383;5,087,571; and 4,736,866.

In an exemplary embodiment, the “transgenic non-human animals” of theinvention are produced by introducing transgenes into the germline ofthe non-human animal. Embryonal target cells at various developmentalstages can be used to introduce transgenes. Different methods are useddepending on the stage of development of the embryonal target cell. Thezygote is the best target for micro-injection. In the mouse, the malepronucleus reaches the size of approximately 20 micrometers in diameterwhich allows reproducible injection of 1-2 pl of DNA solution. The useof zygotes as a target for gene transfer has a major advantage in thatin most cases the injected DNA will be incorporated into the host genebefore the first cleavage (Brinster et al. (1985) PNAS 82:4438-4442). Asa consequence, all cells of the transgenic non-human animal will carrythe incorporated transgene. This will in general also be reflected inthe efficient transmission of the transgene to offspring of the foundersince 50% of the germ cells will harbor the transgene. Microinjection ofzygotes is the preferred method for incorporating transgenes inpracticing the invention.

For construction of transgenic mice, procedures for embryo manipulationand microinjection are described in Hogan et al. Manipulating the MouseEmbryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1986). Similar methods are used for production of other transgenicanimals. In an exemplary embodiment, mouse zygotes are collected fromsix week old females that have been superovulated with pregnant maresserum (PMS) followed 48 hours later with human chorionic gonadotropin.Primed females are placed with males and checked for vaginal plugs onthe following morning. Pseudopregnant females are selected for estrus,placed with proven sterile vasectomized males and used as recipients.Zygotes are collected and cumulus cells removed by treatment withhyaluronidase (1 mg/ml). Pronuclear embryos are recovered from femalemice mated to males. Females are treated with pregnant mare serum, PMS,(5 IU) to induce follicular growth and human chorionic gonadotropin, hCG(51 U) to induce ovulation. Embryos are recovered in a Dulbecco'smodified phosphate buffered saline (DPBS) and maintained in Dulbecco'smodified essential medium (DMEM) supplemented with 10% fetal bovineserum.

Microinjections can be performed, for example, using Narishigemicromanipulators attached to a Nikon diaphot microscope. Embryos areheld in 100 microliter drops of DPBS under oil while beingmicroinjected. DNA solution is microinjected into the largest visiblemale pronucleus. Successful injection is monitored by swelling of thepronucleus. Immediately after injection embryos are transferred torecipient females, mature mice mated to vasectomized male mice.Recipient females are anesthetized using 2,2,2-tribromoethanol.Paralumbar incisions are made to expose the oviducts and the embryos aretransformed into the ampullary region of the oviducts. The body wall issutured and the skin closed with wound clips. Recipients areappropriately ear notched for identification and maintained untilparturition.

To identify transgenic offspring, particularly where conditionaltransgenic systems have been employed such that no phenotypic trait isapparent absent induction, standard tail samples can be used to assessincorporation of the transgene. For example, at three weeks of age,about 2-3 cm long tail samples are excised for DNA analysis. The tailsamples are digested by incubating overnight at 55° C. in the presenceof 0.7 ml 50 mM Tris, pH 8.0, 100 mM EDTA, 0.5% SDS and 350 μg ofproteinase K. The digested material is extracted once with equal volumeof phenol and once with equal volume of phenol:chloroform (1:1 mixture).The supernatants are mixed with 70 μl 3 M sodium acetate (pH 6.0) andthe DNAs are precipitated by adding equal volume of 100% ethanol. TheDNAs are spun down in a microfuge, washed once with 70% ethanol, driedand dissolved in 100 μl TE buffer (10 mM Tris, pH 8.0 and 1 mM EDTA). 10to 20 μl of DNAs were cut with restrictions based on the transgene map,electrophoresed on agarose gels, blotted onto nitrocellulose paper andhybridized with ¹³P-labeled probes described herein.

Retroviral infection can also be used to introduce a Ipf1 transgene intoa non-human animal. The developing non-human embryo can be cultured invitro to the blastocyst stage. During this time, the blastomeres can betargets for retroviral infection (Jaenich, R. (1976) PNAS 73:1260-1264).Efficient infection of the blastomeres is obtained by enzymatictreatment to remove the zona pellucida (Manipulating the Mouse Embryo,Hogan eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,1986). The viral vector system used to introduce the transgene istypically a replication-defective retrovirus carrying the transgene(Jahner et al. (1985) PNAS 82:6927-6931; Van der Putten et al. (1985)PNAS 82:6148-6152). Transfection is easily and efficiently obtained byculturing the blastomeres on a monolayer of virus-producing cells (Vander Putten, supra; Stewart et al. (1987) EMBO J. 6:383-388).Alternatively, infection can be performed at a later stage. Virus orvirus-producing cells can be injected into the blastocoele (Jahner etal. (1982) Nature 298:623-628). Most of the founders will be mosaic forthe transgene since incorporation occurs only in a subset of the cellswhich formed the transgenic non-human animal. Further, the founder maycontain various retroviral insertions of the transgene at differentpositions in the genome which generally will segregate in the offspring.In addition, it is also possible to introduce transgenes into the germline by intrauterine retroviral infection of the midgestation embryo(Jahner et al. (1982) supra).

A third type of target cell for transgene introduction is the embryonalstem cell (ES). ES cells are obtained from pre-implantation embryoscultured in vitro and fused with embryos (Evans et al. (1981) Nature292:154-156; Bradley et al. (1984) Nature 309:255-258; Gossler et al.(1986) PNAS 83: 9065-9069; and Robertson et al. (1986) Nature322:445-448). Transgenes can be efficiently introduced into the ES cellsby DNA transfection or by retrovirus-mediated transduction. Suchtransformed ES cells can thereafter be combined with blastocysts from anon-human animal. The ES cells thereafter colonize the embryo andcontribute to the germ line of the resulting chimeric animal. For reviewsee Jaenisch, R. (1988) Science 240:1468-1474.

Methods of making knock-out or disruption transgenic animals are alsogenerally known. See, for example, Manipulating the Mouse Embryo, (ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986). Anexemplary knock-out mouse is described in the examples below. As set outabove, recombinase-dependent knockouts can also be generated, e.g. byhomologous recombination to insert recombinase target sequences, suchthat tissue specific and/or temporal control of inactivation of theendogenous Ipf1 gene can be controlled as above.

EXEMPLIFICATION

The invention now being generally described, it will be more readilyunderstood by reference to the following examples which are includedmerely for purposes of illustration of certain aspects and embodimentsof the present invention, and are not intended to limit the invention.

EXAMPLE 1 Cloning and Expression of Ipf1

As described below, a cDNA encoding Ipf1, a novel mammalianhomeodomain-containing protein, has been isolated. Ipf1 is apparentlyexpressed predominantly in the β-cells of normal adulst mouse pancreas,and it binds to and transactivates the insulin promoter, providingevidence that Ipf1 is directly involved in the selective β-cellexpression of the insulin gene. In mouse embryos, Ipf1 expression isinitiated prior to hormone gene expression and restricted to the ventraland dorsal walls of primative foregut at positions where pancreas willlater form. The pattern of Ipf1 expression and its ability to stimulateinsulin gene transcription suggests that Ipf1 functions both in theearly specification of the primative gut to a pancreatic fate and in thematuration of the pancreatic β-cell.

The transcriptional activity of the rat insulin I 5′ flanking DNA is toa large extent mediated by the enhancer element which contains bindingsites for a number of trans-acting nuclear proteins that each contributeto the overall activity of the enhancer (German et al., (1992) Genes Dev6:2165-2176). Although the enhancer element is dominant, it haspreviously been shown that the proximal ‘promoter’ sequences have a lowintrinsic cell specific activity (Edlund et al., (1985) Science231:912-916). As described herein, mutation of the P1 promoter siteresults in a 2.5-fold decrease in transcriptional activity of the wholeinsulin 5′ flank. It is also demonstrated that recombinant Ipf1 binds tothe P1 site and is capable of increasing the activity of the completeinsulin 5′ flanking DNA in transiently transfected insulin-producingβTC1 cells and that this transactivation is dependent on the P1 promotersite. Ipf1 can also transactivate multimers of the P1 site linked to aheterologous TATA box in non-βcells. The relatively low degree oftransactivation by Ipf1 of the isolated P1 site probably reflects theneed for multiple transacting factors in the transcriptional regulationof the insulin gene. Since Ipf1 is restricted to the β-cells of adultpancreas and binds to and transactivates the insulin promoter, it isvery likely that Ipf1 in vivo contributes to the β-cell specificactivity of the insulin promoter. Ipf1 may also contribute to otheraspects of the β-cell phenotype.

In the mouse, morphogenesis of the pancreas begins by evagination of theduodenum at the 26 somite stage (e9.5) (Gittes (1992) PNAS 89:1128-1132,but the midgut and adjacent tissue of mouse embryos acquire the abilityto form exocrine pancreas tissue in vitro at about the 8 somite stage.By the 10 somite stage, a region of the gut itself can be identified asthe precursor of exocrine pancreas (Wessells et al. (1967) Dev. Biol.15:237-270). The onset of Ipf1 protein expression at around the 13somite stage supports a role for Ipf1 in the commitment of the primitiveforegut endoderm to a pancreatic fate. At this early stage ofdevelopment, no “pancreatic” mesoderm or even loose mesoderm isassociated with the dorsal gut endoderm which instead is in closeproximity to the notochord (Wessells et al. supra). The notochord isknown as a source of inductive signals that contribute to theregionalization of the neural plate (Yamada et al., (1991) Cell64:635-647); Ericson et al., (1992) Science 256:1555-1560). A putativerole of the notochord in the early inductive events leading to theregionalization of the gut endoderm can now be studied using Ipf1 as amarker.

Since the onset of Ipf1 expression (e8.5) is correlated with thecommitment of the gut endoderm to a pancreatic fate, this early patternof Ipf1 expression may reflect the specification of pluripotentpancreatic stem cells that are the progenitors of all the variouspancreatic cells. However, it has recently been shown that hormone genetranscripts are present at 20 somites, prior to morphogenesis, and thatexocrine gene expression is initiated well after the formation of thepancreatic diverticulum (Gittes et al., supra). These results, whichindicate that the endocrine cells are specified before the exocrineones, may suggest that the early Ipf1-expressing cells are theprogenitors only of the β-cells rather than of all pancreatic cells.

While it is not clear that there exists a precise lineage relationshipbetween the different pancreatic hormone-producing cells, a number ofindependent studies of normal embryonic islet cells and of differentislet tumor cell lines have shown that certain hormones can beco-expressed in the same cells (Yoshinari et al. (1992) Anat Embryol105:63-70; Madsen et al., (1986) J Cell Biol 103:2025-2034; Teitelman etal., (1987) Dev Biol 121:454-466; Alpert et al., (1988) Cell 53:295-308:Herrera et al., (1991) Development 113:1257. These studies have alsosuggested that the terminal differentiation of individual islet celltypes occurs late in development. There is not complete agreement onwhich of the hormones can be colocalized, but taken together the resultsfavor the hypothesis of a common pancreatic endocrine cell lineage(Alpert et al., supra; Herrera et al., supra; Gittes et al. supra). Ithas been suggested that at e15.5, about half of the insulin-producingcells also express glucagon but a different study claims that in themouse there is never any co-expression of these two hormones. Since, asdescribed below, Ipf1 becomes restricted to the insulin-producing cellsvery early in development and since no apparent co-expression of Ipf1and glucagon is observed, these results also suggest that the α- andβ-cells develop independently.

It is noted that expression of XlHbox8 is also restricted to epithelialcells of the duodenum and the developing pancreas, but in adults XlHbox8is only found in the nuclei of the pancreatic excretory ducts: noexpression is evident in the pancreatic islet cells (Wright et al.,(1988) Development 104:787-794. The differences in amino acid sequenceand in the pattern of expression of these proteins suggest that eitherIpf1 is a mouse homolog of XlHbox8 which has diverged both with respectto structure and function, or that there exist at least two relatedhomeodomain proteins which are both involved in pancreas development. Byusing affinity purified antibodies, the experiments described below haveavoided cross-reaction with a putative XlHbox8 mouse homolog. Moreover,IPF1 genomic DNA has been isolated and characterized, but by using theIPF1 homeobox probe in low stringency hybridization these experiments sofar failed to detect any Ipf1-related gene. Similarly, the Xenopus DNAfragment encoding the C-terminal part of the XlHbox8 gene has beenisolated but no cross-hybridization has been detected with the mousegenomic DNA fragment. However, since these results are negative, thepossibility that the mouse genome contains a true XlHbox8 homolog cannotbe excluded, and likewise, neither can alternative splicing be excludedas a way of generating different polypeptides having an identicalhomeodomain.

Other homeodomain proteins, like members of the POU, LIM and Nkx-2families, are expressed at high levels in subsets of adult cell typesand are implicated in transcriptional control in terminallydifferentiated cells (Herr et al.,(1988) Genes Dev 2:1515-1516; Freyd etal., (1990) Nature 344:875-878; Karisson et al., (1990) Nature344:879-882; Price et al., (1992) Neuron 8:241-255). In some aspects,Ipf1 resembles the POU Pit-1/GHF-I protein in that both proteins areselectively expressed in polypeptide hormone-producing cells andtranscriptionally regulate specific hormone genes (Bodner et al., (1988)Cell 55:505-518; Ingraham et al., (1988) Cell 55:519-529). Mutations ofthe Pit-1/GHF-1 gene in dwarf mice result in hypoplasia of thePit-expressing cells, providing evidence for a role of Pit-1 inspecification of these cell types (Li et al., (1990) Nature347:528-533). It is proposed that Ipf1 may have a similar function inthe development of the pancreas.

Moreover, temporal expression pattern of IPF1 resembles that of thelymphoid-specific transcriptional factor Ikaros, the RNA for which ishighly expressed in the early fetal liver and which then starts todecline at e14 (Georgopoulos et al., (1992) Science 258:808-812). It hasbeen argued that the early high level expression of Ikaros is necessaryfor further commitment and differentiation of the pluripotenthematopoietic stem cell, and it has been suggested that the decrease inexpression represents changes in the developmental profile ofhematopoietic progenitors towards a more committed erythroid stage(Georgopoulos et al., supra). Ipf1 may have a similar dual function inthe development of the pancreas and the β-cells.

i) Cloning of cDNAs Encoding IPF1

The islet-cell specific expression of the rat insulin I gene isdependent both on a distal enhancer element and on more proximal“promoter” sequences which do not contribute to the enhancing activity.The rat insulin I gene, for example, contains a short DNA element,TAATGGG, which is located at positions −80 to −74 and which is conservedin the rat, mouse, guinea pig and human insulin promoters (Steiner etal., (1985) Anna Rev Genet).

To isolate the gene encoding the putative transcriptional regulatoryprotein which binds this site, a set of degenerate PCR primers weredesigned that were complementary to a consensus sequence of helix 3 ofknown homeodomain proteins (see Materials and methods). Lacking anyinformation on the possible structure of IPF1, a primer complementary tosequences in the λgt11 vector was used as the second primer in the PCR.These two sets of primers were used in PCR on total phage DNA preparedfrom a phage stock of a βTC1 λgt11 cDNA library. By cloning andsequencing the DNA fragments obtained in the PCR, a 100 bp fragment wasidentified which showed an open reading frame encoding a partialhomeodomain. Using this fragment as a probe, overlapping cDNAs encodinga protein of 284 amino acids with a calculated molecular weight of 31kDa were isolated from the same library.

The encoded protein IPF1 was so named for reasons presented below. Thededuced amino acid sequence revealed a homeodomain which is divergentfrom the Antennapedia prototype and which contained a unique histidinein position 45 of helix 3 (His-190, SEQ ID No. 2). This homeodomain isnot identical to any previously isolated mammalian homeodomain protein,but part of the homeodomain is identical to the known part of thehomeodomain of the XlHbox8 protein from Xenopus laevis (Wright et al.,(1988) 104:787-794) (FIG. 1B). Only the C-termninal part, includingroughly two-thirds of the homeodomain, of XlHbox8 has been reported. Nohomology outside of the homeodomain is observed between these twoproteins. A genomic DNA fragment has been isolated from the leechHelobdella triseralis, which encodes a homeodomain sharing some homologywith the IPF1 and XlHbox8 proteins (Weeden et al., (1990) Nu. Acid Res18:1908). Only the sequence of the homeodomain of this protein, Htr-A2,has been published but it is 86% homologous to the IPF1 homeodomain andhas the characteristic histidine in helix 3. No additional informationis available regarding this protein.

RNA prepared from the IPF1 cDNA template was translated in vitro and theDNA binding specificity of the in vitro translation product wasdetermined using an electrophoretic mobility shift assay (EMSA) and theinsulin promoter P1 site as a probe (Ohlsson et al., (1991) Mol Endocrin5:897-904; see also Materials and Methods below). The in vitrotranslation product bound to the P1 element and migrated to the samerelative position in the gel as IPF1 from the βTC1 nuclear extract.Competition studies with wild-type and mutant P1 sites showed that thein vitro translation product had the same binding specificity as theendogenous IPF1.

As described below, antibodies were raised against the C-terminal halfof the encoded protein, carrying 48 amino acids of the homeodomain. Theobtained antiserum was shown to block binding of nuclear Ipf1 to the P1site, but did not recognize other homeodomain proteins like Is1-1(Karisson et al., (1990) Nature 344:879-882). To show that the clonedcDNA encoded IPF1, antibodies directed against the part of Ipf1 locatedC-terminally to the homeodomain were affinity purified using theglutathione S-transferase (GST) gene fusion system (see Materials andmethods). These affinity purified antibodies, which recognize theC-terminal part but not the homeodomain of IPF1, gave rise to asupershifted complex of nuclear IPF1 bound to the P1 site. Collectively,these results indicate that the isolated cDNA encodes IPF1.

ii) Ipf1 Transactivates the Insulin Promoter

Sequences immediately upstream of the insulin gene TATA box, whichinclude the P1 promoter site, have previously been shown to be ofimportance for the transcriptional activity of the insulin 5′ flankingDNA and to be preferentially active in pancreatic endocrine cell lines(Edlund et al., (1985) Science 230:912-916. It is demonstrated hereinthat a 5′ flank where the AA residues in the TAATGGG IPF1 binding sitehave been changed to CC, and to which IPF1 fails to bind, has a 2.5-foldlower activity than the wild-type 5′ flank in βTC1 cells (FIG. 1A). Thisresult is in contrast to previously published results (Karlsson et al.,(1987) PNAS 84:8819-8823). The activity of the wild-type insulin 5′flank in βTC1 cells was further increased by co-transfection with avector in which Ipf1 expression is under the control of the Rous sarcomavirus (RSV) long terminal repeat (FIG. 1A) and, as expected, the mutant5′ flank could not be transactivated by Ipf1. Ipf1 was also tested tosee if it could transactivate a construct carrying five copies of the P1site linked to the β-globin TATA box in non-pancreatic cells. If Ipf1could transactivate this construct, it should be preferentially activein Ipf1-containing insulin-producing cells. Therefore, the intrinsiccell specificity of this construct was analyzed and found that it was,relative to the control TATA box construct, 3-fold more active in theβTC1 cells than in the CHO cells (FIGS. 1B and 1C). By expressing Ipf1in the CHO cells, the activity of the 5×P1 construct was increased tothat seen in the βTC1 cells (FIG. 1B). The activity of the 5×P1construct could also be increased 2-fold in the βTC1 cells byco-transfection with the RSV-Ipf1 expression vector (FIG. 1C). As aspecificity control, an RSV-Is1-1 expression construct was shown to notbe able to transactivate the 5×P1 β-globin construct in the CHO cells(FIG. 1B).

iii) Ipf1 is Selectively Expressed in the Adult Pancreatic β-cells

Native Ipf1 is detected in nuclear extracts prepared frominsulin-producing βTC1 cells but not in nuclear extracts prepared fromglucagon-producing αTC1 cells or from non-endocrine cells. UtilizingNorthern analysis of RNA prepared from αTC1 cells, βTC1 cells, and avariety of other mouse cell lines and organs, a 2.3 kb IPF1 transcriptwas detected only in βTC1 cells. Ipf1 RNA was also found to be presentin insulin-producing cell lines from other species. As a test of thedifferentiated state of the αTC1 and βTC1 cells used, RNA from thesecells was probed with insulin and glucagon cDNA.IT was observed thatvery little or no co-expression of these genes occurs.

The pattern of expression of IPF1 in adult mouse pancreas was analyzedat the single cell level by immunohistochemistry using affinity purifiedanti-Ipf1 antibodies (see Materials and methods). Immunoreactivity wasreadily detectable within the islets whereas no staining was observed inthe exocrine pancreas or within the duct cells. Within the islets, thestaining paralleled the typical pattern for insulin-producing cellssince the majority of the cells were positive and were all located inthe center of the islets and double immunostaining using anti-IPF1 andanti-hormone antibodies showed that Ipf1 was not present in glucagonandsomatostatin-producing cells. Since IPF1 is apparently restricted to theβ-cells of adult pancreas and since it binds to and transactivates theinsulin promoter, it is very likely that IPF1 is directly involved inthe control of the β-cell specific activity of the insulin gene.

iv) Ipf1 is Selectively Expressed in the Pancreatic Progenitor Cells inEarly Mouse Embryos

The affinity purified anti-Ipf1 antibodies were employed forimmunohistochemistry on cryostat sections of mouse e8.5-15.5 embryos tostudy the temporal and spatial pattern of IPF1 expression at the singlecell level. At all stages of development, Ipf1 expression was onlydetected in the pancreatic anlagen or in the pancreas itself. In bothsagittal and transverse sections of 18-20 somite embryos, IPF1 positivecells are present in the part of duodenum which will later give rise tothe dorsal and ventral pancreas. By using whole-mountimmunohistochemistry (see Materials and methods) it was conclusivelydemonstrated that Ipf1 is only expressed in the dorsal and ventral wallsof the duodenum and not in the lateral parts of the gut wall. Thus, Ipf1expression is restricted to the sites where the dorsal and ventralpancreas will start to evaginate. At the 18-20 somite stage the majorityof the cells in these two regions are IPF1 positive. Moreover, a fewIPF1 positive cells can be detected as early as the 13 somite stage(e8.5) in both the dorsal and ventral walls of the duodenum, whereas noIpf1 positive cells were detected at the 10 somite stage.

In the mouse pancreas a few insulin-containing cells appear around e12in the dorsal bud and a day or so later in the ventral bud.Glucagon-containing cells are already present at e10.5 in the dorsal bud(Herrera et al., (1991) Development 113:1257-1265). Using anti-hormoneantisera and affinity purified anti-Ipf1 antibodies, the pattern ofexpression of Ipf1 was correlated with that of glucagon and insulin. Itwas observed that there was a drastic decrease in the relative number ofIpf1-expressing cells between e10.5 and e11.5. At e13.5 there were stillvery few Ipf1 expressing cells and none or very few of theglucagon-expressing cells express Ipf1. This relative decrease in thenumber of Ipf1 positive cells is most likely the result of ingrowth ofthe exocrine parenchyma which would result in the dispersion of the Ipf1positive cells. At e15.5, the relative number of Ipf1 positive cells hasincreased substantially and at this stage the pancreas contains bothinsulin- and glucagon-producing cells but apparently only theinsulin-producing cells express Ipf1. The increase in the relativenumber of Ipf1-expressing cells between e13.5 and e15.5 correlates witha previous observation of a 20-fold relative increase in the number ofinsulin-producing β-cells during this period (Herrera et al., supra).

v) Materials And Methods

Polymerase Chain Reaction and Isolation of cDNA Clones

The following combinations of oligonucleotides were used in the PCRs: aset of degenerate oligonucleotides complementary to a consensus sequenceof helix III of known homeoboxes, 5′-GCAAGCTTCATIC^(T)/_(G)IC^(T)/_(G)^(G)/_(A)TT^(C)/_(T)TG^(G)/_(A)AACCA-3′, was combined with either of thetwo oligonucleotides included in the λgt11 insert screening amplimer set(cat. no 5412-1, Clontech Laboratories Inc., Palo Alto, Calif.). The DNAtemplate was prepared from a βTC1 λgt11 library (Walker et al., (1990)Nuc. Acid Res. 18:1109-1176. An aliquot of this library was dialyzedagainst distilled water and then frozen, thawed and used in the PCRswhich were carried out using Taq DNA polymerase (Perkin-Elmer/Cetus)according to the manufacturer's instructions. The PCR product ofinterest was sequenced and subsequently labelled with [α-³²P]dATP andused as a probe to screen the βTC)λgt11 in order to isolate afull-length cDNA clone.

Nuclear Extract Preparation and DNA Transfections

Nuclear extract was prepared from βTC1 cells, a transgenically derivedinsulin-producing β-cell line (Efrat et al., (1988) PNAS 85:9037-9041),as previously described (Ohisson and Edlund, (1986) Cell 45:35-44). DNAtransfections of βTC1 and CHO cells were carried out as describedpreviously (Walker et al., (1983) Nature 306:557-581).

In vitro Transcription and Translation

The Is1-1 template for SP6 polymerase-directed in vitro transcriptionhas been described earlier (Ohlsson et al., (1991) Mol Endocrinol5:897-904). The IPF1 template was constructed by inserting thefull-length Ipf1 cDNA into the vector pGEM 3. The template waslinearized before T7 polymerase-directed in vitro transcription. Invitro translation in rabbit reticulocyte lysates was carried out asrecommended by the manufacturer (Promega, Madison, Wis.).

Electrophoretic Mobility Shift Assay

The following oligonucleotides were used in the EMSA: wild-type promoterelement P1: GCCCTTAATGGGCCAAACGGCA; P1 mutant 1: GGGGTTAATGGGCCAAACGGCA;P1 mutant 2: GCCCTTCCTGGGCCAAACGGCA; P1 mutant 3:GCCCTTAATCCCCCAAACGGCA; and wild-type enhancer element E2:GCCCCTTGTTAATAATCTAAT (Ohlsson et al., (1991), supra). Theseoligonucleotides were all custom-made by Symbicom AB (Umea, Sweden). Theoligonucleotides were annealed, end-labelled and purified as previouslydescribed (Ohlsson et al., (1988), supra). The EMSA was carried out asdescribed previously (Ohlsson et al., (1988), supra). The antisera usedwere added together with nonspecific DNA {poly[d(I-C)]:poly[d(A-T)], 1:1ratio} 15-20 min before the specific end labelled synthetic DNAfragment.

Northern Blot Analysis

Poly(A)+ RNA was prepared from the following cell lines: βTC1, αTC1 [atransgenically derived glucagon-producing α-cell line (Efrat et al.(1988) Neuron 1:605-613)], Ltk⁻ (a mouse fibroblast cell line) and J558L[a mouse myeloma (Oi et al., (1983) PNAS 80:825-829)] using the FastTrack kit from Invitrogen Inc. (San Diego, Calif.). Poly(A)+ RNAs fromthe tissues used were purchased from Clontech Inc. (Palo Alto, Calif.).Electrophoresis of RNA, blotting, stripping, hybridization and randomlabelling of probes were performed as described previously (Sambrook etal., (1989) Molecular Cloning: A Laboratory Manual, supra).

Preparation of Antisera

Anti-IPF1 antiserum was prepared using a DNA fragment encoding theC-terminal half of IPF1 which includes part of the homeodomain. Thisfragment was inserted into the expression vector path 11 and expressedas a TrpE fusion protein (Klempnauer and Sippel, (1987) EMBO J6:2719-2725; Angel et al., (1988) Nature 332:166-171). The fusionprotein was purified by preparative SDS-PAGE and used to elicitpolyclonal antibodies in rabbits (Thor et al., (1991) Neuron 7:1-9). Toobtain antibodies that specifically recognized the C-terminal part ofIpf1, the C-terminal part of Ipf1 (amino acids 215-284) lacking anyhomeodomain residues was expressed as a fusion protein with glutathioneS-transferase using the GST gene fusion system in Escherchia coli (Smithand Johnson, (1988) Gene 67:31-40; Pharmacia, Uppsala, Sweden). Thefusion protein was affinity purified on a glutathione-Sepharose 4Bcolumn (Pharmacia, Uppsala, Sweden) and the eluted fusion protein wasimmobilized on Affi-gel 10 (Thor et al., supra). The anti-Ipf1 antiserumwas applied to a column containing the immobilized Ipf1 C-terminalfusion protein; after extensive washing, the bound antibodies wereeluted, reapplied to an identical column and subsequently eluted (Thoret al., supra).

Immunohistochemistry

Immunohistochemistry on adult mouse pancreas was done on freshly frozenmouse C57BL/6JBom (Bomholtgard Breeding and Research Centre Ltd, Ry,Denmark) pancreas that had been sectioned on a cryostat. Cryosections (8μm) were mounted on glass slides, air dried and stored at −80° C. Priorto immunostaining, the sections were fixed in 1% paraformnaldehyde (pH7.4) for 20 min, washed in TBS (50 mM Tris-HCI pH 7.4, 150 mM NaCl) andblocked with 5% normal goat serum in TBST (TBS containing 0.1% TritonX-100) for 10 min. Sectioning of embryos was done by harvesting embryosfrom timed (Kaufman, 1992), pregnant C57BL/6JBom mice that were eitherfixed in 1% paraformaldehyde (pH 7.4) for 1-2 h and then frozen (fore8.5-11.5 embryos) or frozen directly (for e12.5-16.5 embryos). Theimmunohistochemistry on both pancreas and embryos was then carried outas previously described (Thor et al., supra).

Whole-mount Immunohistochemistry

Whole-mount immunohistochemistry was carried out on e8.5-9.5 mouseembryos as described previously (Ruiz I Altaba and Jessel, (1991)Development 112:945-958) but with the following modifications. Embryoswere fixed in 1% paraformaldehyde, 0.1 M potassium phosphate pH 7.4 for1-2 h, transferred to 30% sucrose, 0.1 M potassium phosphate, 0.02%sodium azide and stored at +4 C. Before staining, the embryos weretransferred to TBS for 1 h. The embryos were then blocked for endogenousperoxidase activity in methanol containing 3% hydrogen peroxide for atleast 2 h. The blocking solution was then gradually replaced by TBS.Non-specific binding was reduced by incubation in 5% normal goat serumin TBST. Antibodies were diluted in TBST with 5% normal goat serum. Theprimary antibodies were detected with the ABC immunoperoxidase systemaccording to the manufacturer's recommendation (Vector LaboratoriesInc., USA) with the exception that the ABC complex was diluted 5-foldbefore incubation. After each antibody incubation, embryos wereextensively washed in TBST for at least 2 h with four to six changes.

EXAMPLE 2 Ipf1 Transgenic Mice

In mouse embryos, Ipf1 expression is restricted to the developingpancreatic anlagen and is initiated when the foregut endoderm commits toa pancreatic fate. It is now demonstrated that mice homozygous for atargeted mutation in the Ipf1 gene selectively lack a pancreas. Themutant pups survive fetal development but die within a few days afterbirth. The gastrointestinal part and all other internal organs werenormal in appearance. No pancreatic tissue and no ectopic expression ofinsulin or pancreatic amylase could be detected in mutant embryos andneonates. These findings show that Ipf1 is needed for the formation ofthe pancreas and suggest that Ipf1 acts to determine the fate of commonpancreatic precursor cells and/or to regulate their propagation.

The mammalian pancreas is a mixed exocrine and endocrine gland that, inmost species, arises from ventral and dorsal buds which subsequentlymerge to form the definitive pancreas. In both mouse and rat, the firsthistological sign of morphogenesis of the dorsal pancreas is a dorsalevagination of the duodenum at the level of the liver at around 22-25somite stage, and shortly thereafter a ventral evagination appears as aderivative of the liver diverticulum2-4. Low levels of insulin genetranscripts are already present and restricted to the dorsal foregutendoderm at 20 somites suggesting that pancreas or insulin-gene-specifictranscriptional factors are present in this region prior to the onset ofmorphogenesis.5

In early mouse embryos, the Ipf1 protein is detected only in thedeveloping pancreas but alter in development and in adult mouse pancreasIpf1 is selectively expressed in the β-cells where it binds to andtransactivates the insulin gene. The structurally related XenopusXIHbox86 and rat STF-1/IDX-17,8 proteins, are also selectively expressedin the endoderm of the duodenum and the pancreas but at present it isnot known if these proteins represent functional homologs of Ipf1. Totest the hypothesis that Ipf1 plays a role in the pancreatic commitmentof the foregut endoderm, Ipf1-deficient mice were generated by deletingexon 2, which encodes the homeodomain of Ipf1 using homologousrecombination in ES-cells (FIG. 2). Mice heterozygous for the Ipf1mutation show no apparent abnormalities, they are fertile and theiroffspring show the expected Mendelian frequencies of mutant genotypesindicating that the Ipf1-deficiency does not cause embryonic lethality.However, all homozygous mutant mice die within a few days after birth,showing a complete penetrance of this neonatal mortality phenotype. Thetargeted Ipf1−/− mutant embryos show no detectable Ipf1 immunoreactivityas analyzed by whole-mount immunohistochemistry using anti-Ipf1antibodies.

Newborn homozygous mutant mice do not show any morphologicalabnormalities, except that they appear slightly smaller than wildtypeand heterozygous littermates, on average ˜80% for newborn pups (n=15),and ˜60% for two day old pups (n=15). Most Ipf1-deficient pups areinitially able to feed as indicated by the presence of milk in theirstomachs, but all die within a few days after birth. To determine ifpancreas development was affected in the Ipf1 mutants, histologicalanalyses were performed on new born pups from a cross betweenheterozygous Ipf1 mutants. The homozygous Ipf1 mutants completely lack apancreas but the duodenum from which the pancreas normally developsshowed the normal C-shaped form. The intestines of the Ipf1−/− pups(n=8) have the same relative length (cm/g body weight) +/−10%, as thewildtype pups and show no apparent abnormalities except that the loopsof the small intestine are positioned somewhat differently in theabdomen compared to the wildtype. In the homozygote mutants (n=8) boththe liver, which develops from the same part of the primitive foregut asthe pancreas, and the spleen, which is thought to be derived from“pancreatic” mesoderm, also appear normal and show the same relativeweight (mg/g body weight) +/−10%, as the wildtype. The common bile ductand the ventral pancreatic duct are both derived from the hepaticdiverticulum of the foregut and the main duct of the pancreas normallyfuses with the common bile duct in the duodenal wall and both empty intothe duodenal lumen at the major duodenal papilla. In the homozygousmutants there is no pancreatic duct, but the common bile duct ispresent, indicating that, apart from the lack of a pancreas, theduodenal tract is normally developed. Thus, it may be concluded thatIpf1-deficiency leads to the selective loss of the pancreas. The Ipf1−/−pups that are able to feed and live for more than 2 days show elevatedurine glucose levels, ≧55 mM for three day old Ipf1−/− pups (n=7),suggesting that the cause of death is partly due to insulin deficiency.The lack of the other islet hormones and the exocrine digestive enzymesmay also contribute to the pathology.

The complete lack of a pancreas indicates that Ipf1 is required early inthe development of the pancreas and suggests that Ipf1 acts either atthe level of determination or the early differentiation of the pancreas.In normal mice, pancreatic amylase and insulin are highly andspecifically expressed in the exocrine and endocrine pancreas,respectively, and the expression of the gut-hormone gastrin can be usedto determine the state of differentiation of the intestinal epithelium.To exclude the possibility that in the Ipf1-deficient mice morphogenesiswas arrested but cytodifferentiation still occurred, immunohistochemicalanalysis of mutant and wild-type mouse embryos and neonates wasperformed. In the mouse, both insulin and amylase expressing cells haveaccumulated in sufficiently high numbers in the pancreas at aroundembryonic day e15 to allow reproducible detection byimmunohistochemistry. The intestinal epithelium differentiates late indevelopment so expression of gastrin was monitored, in sections of theduodenum, in newborn animals. No pancreatic tissue was present in mutante15 embryos and neonates and no ectopic expression of insulin andamylase was detected in serial sagital sections of the duodenum ofmutant embryos and neonates. Cells expressing gastrin were present inthe duodenum from both wildtype and mutant newborn animals. This, andthe normal histology of the intestinal epithelium in the mutantsindicate that this part of the duodenum develops normally. The lack ofpancreatic tissue and of ectopic expression of insulin and pancreaticamylase in the developing duodenum show that both cytodifferentiationand morphogenesis of the pancreas is arrested in the homozygous mutants.

The observed phenotype further suggests that Ipf1 has an early functionin the initial stages of pancreas development. A few Ipf1 positive cellscan first be detected in the gut region at around the 10-12 somitestages which is when the foregut endodern commits to a pancreatic fate.This and the lack of a pancreas in the Ipf1-deficient mutants stronglysuggest that Ipf1 functions in the determination and/or maintenance ofthe pancreatic identity of common precursor cells, or in the regulationof their propagation.

All of the above-cited references and publications are herebyincorporated by reference.

Equivalents

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

9 1313 base pairs nucleic acid both linear cDNA unknown CDS 128..979 1CAGGAGAGCA GTGGAGAACT GTCAAAGCGA TCTGGGGTGG CGTAGAGAGT CCGCGAGCCA 60CCCAGCGCCT AAGGCCTGGC TTGTAGCTCC GACCCGGGGC TGCTGGCCCC AAGTGCCGGC 120TGCCACC ATG AAC AGT GAG GAG CAG TAC TAC GCG GCC ACA CAG CTC TAC 169 MetAsn Ser Glu Glu Gln Tyr Tyr Ala Ala Thr Gln Leu Tyr 1 5 10 AAG GAC CCGTGC GCA TTC CAG AGG GGC CCG GTG CCA GAG TTC AGC GCT 217 Lys Asp Pro CysAla Phe Gln Arg Gly Pro Val Pro Glu Phe Ser Ala 15 20 25 30 AAC CCC CCTGCG TGC CTG TAC ATG GGC CGC CAG CCC CCA CCT CCG CCG 265 Asn Pro Pro AlaCys Leu Tyr Met Gly Arg Gln Pro Pro Pro Pro Pro 35 40 45 CCA CCC CAG TTTACA AGC TCG CTG GGA TCA CTG GAG CAG GGA AGT CCT 313 Pro Pro Gln Phe ThrSer Ser Leu Gly Ser Leu Glu Gln Gly Ser Pro 50 55 60 CCG GAC ATC TCC CCATAC GAA GTG CCC CCG CTC GCC TCC GAC GAC CCG 361 Pro Asp Ile Ser Pro TyrGlu Val Pro Pro Leu Ala Ser Asp Asp Pro 65 70 75 GCT GGC GCT CAC CTC CACCAC CAC CTT CCA GCT CAG CTC GGG CTC GCC 409 Ala Gly Ala His Leu His HisHis Leu Pro Ala Gln Leu Gly Leu Ala 80 85 90 CAT CCA CCT CCC GGA CCT TTCCCG AAT GGA ACC GAG CCT GGG GGC CTG 457 His Pro Pro Pro Gly Pro Phe ProAsn Gly Thr Glu Pro Gly Gly Leu 95 100 105 110 GAA GAG CCC AAC CGC GTCCAG CTC CCT TTC CCG TGG ATG AAA TCC ACC 505 Glu Glu Pro Asn Arg Val GlnLeu Pro Phe Pro Trp Met Lys Ser Thr 115 120 125 AAA GCT CAC GCG TGG AAAGGC CAG TGG GCA GGA GGT GCT TAC ACA GCG 553 Lys Ala His Ala Trp Lys GlyGln Trp Ala Gly Gly Ala Tyr Thr Ala 130 135 140 GAA CCC GAG GAA AAC AAGAGG ACC CGT ACT GCC TAC ACC CGG GCG CAG 601 Glu Pro Glu Glu Asn Lys ArgThr Arg Thr Ala Tyr Thr Arg Ala Gln 145 150 155 CTG CTG GAG CTG GAG AAGGAA TTC TTA TTT AAC AAA TAC ATC TCC CGG 649 Leu Leu Glu Leu Glu Lys GluPhe Leu Phe Asn Lys Tyr Ile Ser Arg 160 165 170 CCC CGC CGG GTG GAG CTGGCA GTG ATG TTG AAC TTG ACC GAG AGA CAC 697 Pro Arg Arg Val Glu Leu AlaVal Met Leu Asn Leu Thr Glu Arg His 175 180 185 190 ATC AAA ATC TGG TTCCAA AAC CGT CGC ATG AAG TGG AAA AAA GAG GAA 745 Ile Lys Ile Trp Phe GlnAsn Arg Arg Met Lys Trp Lys Lys Glu Glu 195 200 205 GAT AAG AAA CGT AGTAGC GGG ACC CCG AGT GGG GGC GGT GGG GGC GAA 793 Asp Lys Lys Arg Ser SerGly Thr Pro Ser Gly Gly Gly Gly Gly Glu 210 215 220 GAG CCG GAG CAA GATTGT GCG GTG ACC TCG GGC GAG GAG CTG CTG GCA 841 Glu Pro Glu Gln Asp CysAla Val Thr Ser Gly Glu Glu Leu Leu Ala 225 230 235 GTG CCA CCG CTG CCACCT CCC GGA GGT GCC GTG CCC CCA GGC GTC CCA 889 Val Pro Pro Leu Pro ProPro Gly Gly Ala Val Pro Pro Gly Val Pro 240 245 250 GCT GCA GTC CGG GAGGGC CTA CTG CCT TCG GGC CTT AGC GTG TCG CCA 937 Ala Ala Val Arg Glu GlyLeu Leu Pro Ser Gly Leu Ser Val Ser Pro 255 260 265 270 CAG CCC TCC AGCATC GCG CCA CTG CGA CCG CAG GAA CCC CGG 979 Gln Pro Ser Ser Ile Ala ProLeu Arg Pro Gln Glu Pro Arg 275 280 TGAGGACAGC AGTCTGAGGG TGAGCGGGTCTGGGACCCAG AGTGTGGACG TGGGAGCGGG 1039 CAGCTGGATA AGGGAACTTA ACCTAGGCGTCGCACAAGAA GAAAATTCTT GAGGGCACGA 1099 GAGCCAGTTG GATAGCCGGA GAGATGCTGCGAGCTTCTGA AAAAACAGCC CTGAGCTTCT 1159 GAAAACTTTG AGGCTCGCTC TGATGCCAAGCTAATGGCCA GATCTGCCTC TGAGGACTCT 1219 TTCCTGGGAC CAATTTAGAC AACCTGGGCTCCAAACTGAG GACAATAAAA AGGGTACAAA 1279 CTTGAGCGTT CCAATACGGA CCAGCAGGCGAGAG 1313 284 amino acids amino acid linear protein unknown 2 Met AsnSer Glu Glu Gln Tyr Tyr Ala Ala Thr Gln Leu Tyr Lys Asn 1 5 10 15 ProCys Ala Phe Gln Arg Gly Pro Val Pro Glu Phe Ser Ala Asn Pro 20 25 30 ProAla Cys Leu Tyr Met Gly Arg Gln Pro Pro Pro Pro Pro Pro Pro 35 40 45 GlnPhe Thr Ser Ser Leu Gly Ser Leu Glu Gln Gly Ser Pro Pro Asp 50 55 60 IleSer Pro Tyr Glu Val Pro Pro Leu Ala Ser Asp Asp Pro Ala Gly 65 70 75 80Ala His Leu His His His Leu Pro Ala Gln Leu Gly Leu Ala His Pro 85 90 95Pro Pro Gly Pro Phe Pro Asn Gly Thr Glu Pro Gly Gly Leu Glu Glu 100 105110 Pro Asn Arg Val Gln Leu Pro Phe Pro Trp Met Lys Ser Thr Lys Ala 115120 125 His Ala Trp Lys Gly Gln Trp Ala Gly Gly Ala Tyr Thr Ala Glu Pro130 135 140 Glu Glu Asn Lys Arg Thr Arg Thr Ala Tyr Thr Arg Ala Gln SerSer 145 150 155 160 Glu Leu Glu Lys Glu Phe Leu Phe Asn Lys Tyr Ile SerArg Pro Arg 165 170 175 Arg Val Glu Leu Ala Val Met Leu Asn Leu Thr GluArg His Ile Lys 180 185 190 Ile Trp Phe Gln Asn Arg Arg Met Lys Trp LysLys Glu Glu Asp Lys 195 200 205 Lys Arg Ser Ser Gly Thr Pro Ser Gly GlyGly Gly Gly Glu Glu Pro 210 215 220 Glu Gln Asp Cys Ala Val Thr Ser GlyGlu Glu Leu Leu Ala Val Pro 225 230 235 240 Pro Leu Pro Pro Pro Gly GlyAla Val Pro Pro Gly Val Pro Ala Ala 245 250 255 Val Arg Glu Gly Leu LeuPro Ser Gly Leu Ser Val Ser Pro Gln Pro 260 265 270 Ser Ser Ile Ala ProLeu Arg Pro Gln Glu Pro Arg 275 280 29 base pairs nucleic acid singlelinear cDNA unknown 3 GCAAGCTTCA TNCKNCKRTT YTGRAACCA 29 22 base pairsnucleic acid single linear cDNA unknown 4 GCCCTTAATG GGCCAAACGG CA 22 22base pairs nucleic acid single linear cDNA unknown 5 GGGGTTAATGGGCCAAACGG CA 22 22 base pairs nucleic acid single linear cDNA unknown 6GCCCTTCCTG GGCCAAACGG CA 22 22 base pairs nucleic acid single linearcDNA unknown 7 GCCCTTAATC CCCCAAACGG CA 22 21 base pairs nucleic acidsingle linear cDNA unknown 8 GCCCCTTGTT AATAATCTAA T 21 16 base pairsnucleic acid single linear cDNA unknown 9 GCCCTTAATG GGCCAA 16

I claim:
 1. An isolated or recombinant nucleic acid encoding arecombinant insulin promoter fator 1 (Ipf1) polypeptide comprising apolypeptide sequence at least 90% identical to an amino acid sequencerepresented in SEQ ID NO: 2, wherein said polypetide modulates at leastone of proliferation, differentiation or survival of a cell whichexpresses a gene that is transcriptionally regulated by anIpf1-responsive element (Ipf1-RE).
 2. The nucleic acid of claim 1,wherein said nucleotide sequence hybridizes under conditions including awash step of 0.2×SSC at 50° C. to a nucleic acid probe having a sequencerepresented by at least 12 consecutive nucleotides of SEQ ID NO:
 1. 3.The nucleic acid of claim 1, wherein said nucleotide sequence hybridizesunder conditions including a wash step of 0.2×SSC at 50° C. to a nucleicacid probe having a sequence represented by at least 12 consecutivenucleotides between nucleotide residues 31 to 562 or 761 to 979 of SEQID NO:
 1. 4. The nucleic acid of claim 1, further comprising atranscriptional regulatory sequence operably linked to said nucleotidesequence so as to render said nucleic acid suitable for use as anexpression vector.
 5. An expression vector, capable of replicating in atleast one of a prokaryotic cell and eukaryotic cell, comprising thenucleic acid of claim
 1. 6. A host cell transfected with the expressionvector of claim 5 expressing said recombinant polypeptide.
 7. Thenucleic acid of claim 1, wherein the Ipf1 polypeptide sequence is atleast 95% identical to an amino acid sequence represented in SEQ ID NO:2.